Greetings, everyone!
Here's everything I managed to gather about this game while getting all of the achievements.
I'm sure that I have made a few mistakes somewhere, and if you find any or if you have anything to add, leave a comment and I'll gladly update the guide.
I suggest only using the information here if you are stuck and can't take it anymore; else, it will spoil all the fun.
If you want to get all the achievements, complete the game once, to get the hang of things, and read this before the second play-through.
Good luck, and enjoy!

Gettin' On With the Job: Slay 10 enemies with Marine.
Takin' Off: Slay 100 enemies with Marine.
Marine Killing Machine: Slay 500 enemies with Marine.

Karate Baby: Use Benoit's hand techniques 5 times.
Karate Kid: Use Benoit's hand techniques 50 times.
Jun Tsu Ka Rah God: Use Benoit's hand techniques 200 times.
You have to use Benoit's Wind Hand, iron Hand and Slash Hand skills.

Karine Killing Fields: Slay 500 enemies with Karine.
I Can Kill Too: Slay 50 enemies with Hirado.
Pick easy fights, and defend with those that you do not need kills with.

Myst Veteran: Be in 1000 fights.
You can escape a fight and it still counts.

Fairy Whisper: Use Jeanne for the first time.
Fairy Party: Summon Jeanne 50 times.

I've Got a Gut Feeling: Benefit from Marine's Gut 5 times.
If Marine is knocked out, she will get back in fight in the next round, if there is at least 1 other party member standing. This can only happen once per encounter.

Creator of a Better World: Successfully use Karine's Craft 5 times.
Karine can use her skills to make something better of a few items found around Myst.
She can use the Titan Skin, which is a certain drop from the Rogue, to craft a Titan Corset or Titan Great Corset if she has been promoted.
She can use the Titan Tooth, which has a chance to drop from the Rogue (you may have to save and kill him a few times before it drops), to craft a Rogue Hatchet.
She can repair the Broken Paladin Helmet, that you can buy from Dahl in Green Grass, resulting in a Paladin Helmet.

She can use the Ebony Stick, found in the Eastern Land of Myst, to craft a Defensive Trident.

She can use the Long Bone, found in Rogue Territory, to craft an Ivory Lance.

She can use the Broken Lamp, found in the Dewon Crypt, to create a Djinn Lamp.

Use the Djinn Lamp in the Dewon Crypt to reveal quite a few orbs. Also, you can go back to the bridge, where Secret Room #1 is, and get all of the orbs that might have appeared when you used the lamp. If there are no orbs, use it again just to make sure.

The Baroness: Promote Karine to Baroness.
In order to be able to promote her to Baroness you have to obtain the Seal of the Oak, found in a locked chest in Scarlet River. To open a locked chest you must have the Magical Key equipped.

To promote her you need to go to one of the temples. There is one located in the most western part of the Myst (world map).

We Need Not A Bigger Boat: Slay the Rogue.
We Don't Need An Exorcist Either: Slay the Djinn.
Bear King Slaughterer: Slay Bear King.
Crocodile King Slaughterer: Slay Crocodile King.
Golem King Slaughterer: Slay Golem King.
Lord of The Ants Slaughterer: Slay Lord of the Ants.
Lord of the Roots Slaughterer: Slay Lord of the Roots.
Queen Bee Slaughterer: Slay Queen Bee.
Rat King Slaughterer: Slay Rat King.
Twin Tigers: Slay Twin Tigers.
Kaiserslautern: Slay all the animal kings.

Everybody Has To Start: Complete 1 quest.
Progressive Gamer: Complete 6 quests.
Catch the Wind: Complete Quest #03.
Not Just About Meditation: Complete 30 quests with Hirado. You must only complete the main story quests before Hirado joins your party. Only after he does, complete all the rest.
Quest God: Complete all quests. You must complete Quest #11 before Quest #12. In other words, you have to slay the Chantefleur Ghost while you are on Jack's and James' quest to find their purse. Don't skip it, you can't slay the ghost later.

Curiosity: Find 5 items.
The Examiner: Find 50 items.

More Items for Me: Acquire all items from the secret Forge.
The Forge will only appear on the world map after you have found it.

You can buy special items from the Forge at different times throughout your campaign. You must buy each item before progressing or else you won't be able to buy the rest.
Visit the Forge for the first time when you leave Green Grass Fields and buy the Intuition Pendant. If you do not have any money, farm until you get enough, buy the item, then advance.
After Benoit joins your party, a new item becomes available: the Eagle Ring. Buy that as well.
After talking to Olbar and leaving Festina, before going to look for the rebel, visit the Forge again and buy the Magical Key which will allow you to open locked chests.
When Karine joins your party, go back again and buy the Splash Box.
And once again, after visiting the Monastery, go and buy the Morning Star before proceeding.
If you return to the Forge later, and only if you have bought all of the other items, you will get Fairy Love as a reward for your support.

Discovering Myst: Collect 10 orbs.
Speed Orb Collector: Collect 100 Speed Orbs.
Resistance Orb Collector: Collect 100 Body Orbs.
Mana Orb Collector: Collect 100 Magic Orbs.
Strength Orb Collector: Collect 100 Strength Orbs.

Baby Indy: Find 1 secret room.
Kid Indy: Find 5 secret rooms.
Great Explorer: Find 20 secret rooms.
Indy Jones Learned From Me: Find all secret rooms.

Talkative Leader: Use Marine's Talk 10 times. The option should be something like this: "What am I supposed to do now...?"
The First Step: Play for 1 hour.
The Strategist: Change Marine's Strategy 10 times.
Millennium Addict: Spend 20 hours on one campaign.
Better Safe Than Sorry: Save 100 times.
Myst'Rockfeller: Hold more than 30000 gold.
Patient Traveller: Never use "Go Through" until the end of the game. This refers to the Gray Cave, Rocky Paths and the Scarlet River. You will get the achievement right before the credits.
Sherlock Learned From Me: Complete the game after having completed all quests, found all secret rooms and slain all animal kings. You will get the achievement right before the credits.
Great Samaritan: Complete the game on Hard Mode.
Master of Time: Complete the game in less than 10 hours on Hard Mode. You only need to complete the story related quests.

Quest #01: Find Florette's Teddy Bear
Talk to Florette in Green Grass.

Get the Pink Teddy Bear in Green Grass Fields.

Give the teddy bear to Florette.
Reward: The happiness of a child.

Quest #02: Find Perfect Honey
Talk to Sabor in Green Grass Fields.

Complete Quest #32 to get Perfect Honey.
Give the honey to Sabor.
Reward: You may choose your reward. Pick Strawberry Lollipop if you want to access the Toy Hall and complete all the quests.

Quest #03: Find Bokden
Talk to Bokden in the Guild of Strength.

After that, go look for Bokden in the Rocky Paths and talk to him.

And again in Marshlands of Myst.

And once again in a house in Green Grass Fields.

And then in Sapphire Caves.

And last time in Green Grass.

Reward: Sheep's Wonderfood, Ant Gem, gold and consumables.

Quest #04: Restore the Orb of Valour
Click on the Green Grass Shrine in Green Grass Fields.

Get the Orb of Valour from a chest in the Monastery, next to Sanaris.

Place the orb at the Green Grass Shrine.
Reward: +20 HP to all party members.

Quest #05: Slay the Animal Kings
Talk to Florian in Green Grass Fields.

Slay at least 6 of the animal kings.
Talk to Florian again.
Reward: ...

Quest #06: Complete the Ceremony of Clouds
Get the Blue Fire found in the Guild of Speed. Must have Benoit in your party.

Get the Black Fire found in the Grey Cave. Must have Karine in your party.

Get the White Fire found in Rocky Paths. Must have Hirado in your party.

Get the Red Fire found in Sapphire Caves.

Place each fire on each of the four pillars in the Rocky Paths.

Reward: Open the chest that spawns to get the Cloud Hat.

Quest #07: Find Steiner's Medal
Talk to Steiner in the Guild of Strength.

Get the Golden Medal, found near a lake in the Midlands of Myst.
Give the medal to Steiner.
Reward: Seal of the Brave.

Quest #08: Take Herbal Treatment to Grandpa
Make your way to Pinerock and give the treatment to Grandpa Allen.

Reward: 100 gold.

Quest #09: Find 10 Purple Grapes
Talk to Frank in Pinerock.

Find and collect 10 Purple Grapes that are scattered around the Scarlet River.

Give the grapes to Frank.
Reward: 400 gold.

Quest #10: Find 10 Green Snakes
Talk to Thomas in Pinerock.

Equip the Scaled Gloves and catch 10 Green Snakes that you can find around Green Grass Fields.

Give the snakes to Thomas.
Reward: Snake Suit.

Quest #11: Slay the Chantefleur Ghost
Kill the ghost in Chantefleur Woods.
Strategy: Attack with Jeanne and defend with Marine. Heal Marine when needed.

Reward: Chantefluer Tear. Talk to Jack at the entrance of the woods and he will also give you a Thick Leather Coat.

Quest #12: Find Purse for Jack and James
Talk to Jack and James in Pinerock.

Go to the woods and find their purse.
Give the purse to Jack and James.
Reward: ...

Quest #13: Find the Pillars of Power
Find and interact with all 4 pillars. The Pillar of Mind is found in Secret Room #23.

The Pillar of Strength is found in Secret Room #03.

The Pillar of Speed is found in Rogue's Territory.

The Pillar of Resistance is found in Sapphire Caves.

Reward: +10 to each respective stat to all party members when you interact with each pillar, as well as +10 HP when the quest is done.

Quest #14: Find at least 70 Magic Orbs
Talk to Nathanael in the Guild of Mind.

Find at least 70 Magic Orbs.
Talk to Nathanael again.
Reward: Fractal Headphone.

Quest #15: Talk to Olbar
Go to Festina and talk to Olbar.

Reward: Hope ( ... priceless).

Quest #16: Find Cute Dress
Talk to Nanette in Festina.

Get the Cute Dress found in Karine's house.

Give the dress to Nanette.
Reward: Toy Hall revealed.

Quest #17: Find Festina Goat
Talk to Leon in Festina.

Get the Yummy Cheese from The Refuge.

Get the Festina Goat from the Rocky Paths.

Give the goat to Leon.
Reward: Dam'bl'don Bell.

Quest #18: Find 6 Fat Frogs
Talk to Joey in Festina.

Collect the 6 Fat Frogs from the most western map of Green Grass Fields; those are the only frogs you can collect.

Give the frogs to Joey.
Reward: Exquisite Dinner.

Quest #19: Heal Tibor's Old Legs
Talk to Tibor in a house in Festina.

Get the Youth Wine from Sapphire Caves.

Give the wine to Tibor.
Reward: Ruby Heart or Maturing Potion.

Quest #20: Show Albert the Map to the House of Alchemy
Talk to Albert in Festina.

Get the Map to House of Alchemy from The Refuge.

Show the map to Albert.
Reward: ...

Quest #21: Find Janine's Ring
Talk to Janine in the Guild of Resistance.

Get Janine's Ring from Marshlands of Myst.

Give the ring to Janine.
Reward: Autumn Bud.

Quest #22: Find the Rebel
Find Karine at her house in Bogobaka and talk to her.
Reward: Karine joins your party.

Quest #23: Help the Crying Ghost
Find the Crying Ghost in Bogobaka.

Give the Chantefleur Tear to the ghost.
Reward: +1 level to all party members.

Quest #24: Slay the Rogue
Follow Karine's instructions to find and slay The Rogue.
Strategy: Use Benoit's Iron Hand and Karine's Scare to incapacitate the Rogue. Summon Jeanne as well and use her to heal when necessary. Depending on your level, it might take a couple tries.

Reward: Titan Tooth (doesn't always drop), Titan Skin and Karine joins your forces.

Quest #25: Win the Alchemy Contest
Get Shamfrouil from Bogobaka.

Get Granite Petal from the Rocky Paths.

Get Mesmer Salad from Secret Room #10.
Get Papatapio Root from the Scarlet River.

Complete Quest #21 to get the Autumn Bud.
Talk to Heptitus in the House of Alchemy to take part in the contest.
Reward: Amazing Hat of Alchemy.

Quest #26: Find Hirado
Talk to Sanaris in the Monastery to learn about Hirado.

Find and talk to Hirado in the Sapphire Caves.

Reward: Hirado joins your party.

Quest #27: Slay the Djinn
Go to the Ancient Temple and slay the Djinn.
Strategy: Use Karine’s Martial Mind and Hirado’s Barrier. Spells will not wake him up if he is asleep. Summon Jeanne as well.

Reward: Hirado joins your forces.

Quest #28: Respecting the Ancient Civilization
You will automatically complete this quest after you have slain the Djinn and left the Ancient Temple.

Reward: ...

Quest #29: Slay Queen Bee
Find and slay the Queen Bee in Midlands of Myst.

Reward: Perfect Honey

Quest #30: Slay Rat King
Find and slay the Rat king in the Sapphire Caves.

Reward: ...

Quest #31: Slay Bear King
Find and slay the Bear King in Marshlands of Myst.

Reward: ...

Quest #32: Slay King of the Ants
Find and slay the King of the Ants in the Rocky Paths.

Reward: ...

Quest #33: Slay King of the Felines
Find and slay the Twin Tigers in Marshlands of Myst.

Reward: Hatchet of the Ancients

Quest #34: Slay Golem King
Find and slay the Golem King in the Grey Cave.

Reward: Hero Key and Reflex Glove

Quest #35: Slay Lord of the Roots
Find and slay the Lord of the Roots in the Scarlet River.

Reward: ...

Quest #36: Slay Crocodile King
Find and slay the Crocodile King in Rogue's Territory.

Reward: King Croc Mail

Quest #37: Getting all 11 Butterflies of Life
Find and collect at least 11 out of the 12 butterflies. One can be found in Green Grass Fields.

One in the Shrine in Midlands of Myst.

One in Secret Room #24.

One in the Scarlet River.

Two in Rocky Paths.


One in Rogue's Territory.

Three in Secret Room #07.

One in Sapphire Caves.

And one in the Ancient Temple.

Reward: +10 HP to all party members for every butterfly collected as well as +10 HP when the quest is done.

Quest #38: Get into Toy Hall
Go in the Toy Hall and give the Strawberry Lollipop to Saw Kool, the clown.

Reward: access to the Toy Hall.

Quest #39: Find Cracked Mirror
Talk to the ghost guarding the Dewon Crypt.

While Marine is angry, talk to Isabelle in the General Store of Mystrock.

You can use Swamp Pimento on Marine. It has a chance to make her angry, but make sure you don't have any item equipped that would prevent that. You will find three Swamp Pimento in Bogobaka.

You will get the Cracked Mirror. Give it the ghost in the crypt.
Reward: Access to the Dewon Crypt.

Quest #40: Show Thieves Den Map to Martial
Start: Talk to Martial in Pinerock.

Get the Map to Thieves Den, which is a random drop from all the thieves.
Tell Martial the location of the den.
Reward: 15 gold.

Secret Room #01: in Green Grass Fields, to the east, on the bridge.

Secret Room #02: in Chantefleur Woods, north-east.

Secret Room #03: in Rocky Paths, north of the umbrella.

Secret Room #04: in Rocky Paths, in one of the windmills.

Secret Room #05: in Rocky paths, south-east of the windmills.

Secret Room #06: in Rocky Paths, on one of the highest pillars.

Secret Room #07: it is one of the two secret locations that the ghost boatman can take you to.

Secret Room #08: it is one of the two secret locations that the ghost boatman can take you to.

Secret Room #09: in Secret Room #08. Should be called a Super Secret Room. You need the Air Sandals to jump there.

Secret Room #10: in the swamp, close to the entrance.

Secret Room #11: in the Monastery.

Secret Room #12: in the Monastery, same room as Sanaris.

Secret Room #13: in the lower Rocky Paths, to the south-east.

Secret Room #14: in Rocky Paths, where you find and rescue Balnard.

Secret Room #15: in Sapphire Caves, go up the biggest ladder.

Secret Room #16: in the Ancient Temple, north-east.

Secret Room #17: in the Ancient Temple, to the east.

Secret Room #18: in the Ancient Temple, to the east, as far as you can get.

Secret Room #19: in the Ancient Temple, before heading east.

Secret Room #20: to the right as you are about to enter the Ancient Temple.

Secret Room #21: in the Gray Cave.

Secret Room #22: in the Thieves Den.

Secret Room #23: in the Guild of Mind.

Secret Room #24: in the General Store of Mystrock.

Here's where you can find some of the other items not mentioned above:

The Air Sandals, that allow you to jump higher, are found in the lower Rocky paths.

You can fight some ants in Chantefleur Woods to get an Ant Gem.

The Articulate Shoulder can be found in a chest in the Scarlet River.

The Chantefleur Hood can be found in a chest near the Chantefleur Ghost.

The First Aid Box can be found in a house in Bogobaka.

The Jouvencelle can be found in a chest in the Toy Hall.

The Lizard Mail can be found in a chest in the Scarlet River.

The Mithril Armor can be found in a chest in Rocky Paths.

The Myst Bag, which you must have equipped in order to see the Butterflies of Life, can be found in a chest in Sapphire Caves, east from the place with the Red Fire.

The Nobble Ring, which allows you to sell your items for more if you have it equipped, can be found in the Armory.

The Power Bandana can be found in the Gray Cave.

A Reflex Glove can also be found in a locked chest in Green Grass Fields, on the bridge.

You can fight a few waves of angry monsters in the Sapphire caves, in Secret Room #20, to obtain the Saint Sword.

The Shepherd's Hat can be found in a chest in Pinerock.

The Skewer Javelin can be found in the Marshlands of Myst, to the north.

A Swamp Mineral can be found in a chest in the Sapphire Caves, next to the one with the Myst Bag.