Violator vs Lightning:
Violator:

• Has huge range
  
• Can shot one target for long time - thus do more shots/dmg per wave
  
• Can also crit for 150% if perked (10% chance)

Lightning:

• A bit smaller dmg
  
• Small range
  
• Has a mini-stun (noticeable with perks)
  
• Can do up to 50% more dmg if perked (1% dmg per 2% mobs health missing)
  
• Hits up to 2 more targets (for 50/25% dmg) on higher ranks (so up to 75% more dps than in table)

Gatling and Flamer
Both have really high dps in the spreadsheet, but its not really that good:

• Its single target (only Gatling - Flamer is AOE)
  
• Will be as high only on targets with no armour
  
• Can be cut down to even zero if mobs armour is high and tower rank/dmg is low

Penetrator and Flash
Their dps is calculated for single target, but both towers can hit lots of targets at once if maze/skills/towers supporting are chosen wisely. Thus those can be best dps in game if done right.

Flash and Lightning
Both have mini-stun which upgraded with perks and with help of slowing towers can basically mean a small kill zone from which nothing can run away, while still getting huge aoe dps (especially on Flash or rank 3 Lightnings).

Amp Field and Black Hole
Personally never used any of those. Slow + Flash (with upgraded stun) kinda does the same thing as Black Hole. And slow towers out dps-boost Amp Field while also helping with use of skills. Thou it is worth mentioning that chart says Black Hole doesn't rise dps - which is true - as tower itself doesn't do that. But it is possible that few of them could gang up mobs in nice clusters for aoe towers like Flash to nuke down - thus more mobs - better dps out of such towers.

Perks in red:
You cant go wrong with those.

• Up to 20% dmg/dps gain on physical/elemental towers.
  
• Free tower bases helping with set-up of maze on starting waves.
  
• Up to 10% more slow (the more % slow tower has before adding this the more % dps boost gained - with 10% from perks and 25% on Slow Field rank 1 (giving the least % slow) - we gain 20% dps - up to over 100% more dps for Karios rank 3).
  
• Up to 30% range on skills.
  
• Up to 30% shorter skills recharge.
  
• Up to 10% more dmg/dps from amp towers (survival + multiplicative stacking of Charger).

Perks in orange:
Those are good, but not as much as red ones.

• 150% dmg crits on physical towers, but only 10% chance - so overall around 5% dps gain.
  
• 1% dmg boost for each 2% mobs health missing - technically up to 50% dmg/dps gain. It's better help for fast towers. Huge dmg ones 1/2-shot most mobs so there is really no gain. Low dmg/fast shooting towers will slowly gain more and more dmg - but avg wont be probably higher than 20% anyway.
  
• Boxes with 20 cash that spawn randomly - and that can mean no spawns on even 200 mobs survival wave, or 2-4 spawns on just 20-30 mobs wave - all in hands of RNG-Jesus.
  
• Small dmg over time on control skills like freeze/time reverse - can help on normal, less on hard, totally useless on survival.

Perks in blue:
20% range gain on physical/elemental towers can help towers with big range to keep shooting on wider range.

• Helpful mainly for Violators and less for Mortars/Anti Air - still viable thou.
  
• At least from what I saw - it doesn't really help other towers much. As most of them still can shot over 2 lines without it (I mean tower-path-wall-path).
  
• Could add a bit to Flash cone dmg range - to aoe dps/stun more mobs including air - but personally I saw more use in spending those points somewhere else (like on better slow).

Perks in gray:
If you want to know my honest opinion - they are crap.

• Never liked idea of completely changing maze between waves. Especially on limited number of tower loads we can take (just 4). But you need those if you want to reach the last economy perk.
  
• Adding 1000 dmg to slows/black holes can seem a nice idea especially for normal. Thou if you add 10 seconds delay (which means just 100dps) and consider survival it gets really useless. But if you go full effects tree - its always a small bonus and for me its better than reducing tower sell penalties.

Perks in green:
Those can be as good as read ones, but are really situation/build/maze dependant.

• Armour penetration skill can be a huge dps gain, but only if our maze consists of lots of fast shooting low dmg per shot towers, else its a lost perk point and skill slot. Not useful for survival.
  
• 40 dmg for each 100 dmg done - basically a zone 40% dps booster. In some set-ups could mean a huge dmg gain, for me thou was a lost perk point. Technically could be used in survival with Ke-Weapons (to rise those 5% total hp skills dmg to 7%).
  
• 2 more cash for each kill for 16 seconds if used right can easily mean a decent cash flow. Could help with perfecting normal/hard runs - but as the 20 cash random spawn perk - it can be just useless for survival (especially when staking Chargers you can rank 3 all towers quite early).
  
• 5% mobs total hp as bonus dmg for 3 skills (no clue why it says Lightning - as it means Thunderbolt skill not Lightning tower) can mean a lot. Build a maze that is good against low hp/low armour targets - and finish high hp/armour ones using those 3 skills. If you build maze right way - technically its the only perk that allows you to make a maze that scales good with survival waves - if you build a maze in such a away that you will manage to use those 3 skills 20 times to give you a total of 100% mobs hp bonus dmg done - it wouldn't matter how much waves there will be as you will always be able to kill whole wave.
  
• Stuns and control stuff lasting longer can be a great perk. If you go Flash/Lightning maze - longer stuns are really noticeable and with slows can basically mean a full stun-lock kill zones. Longer crowd controls like freeze/reverse gravity/black hole can be useful too, but personally I used them mostly as means of cancelling mutation/heal mobs spell casts thus their length didn't matter for me - also I didn't spot length difference for holes from Black Hole towers while testing them for this guide.

Game is really cheap - especially if you manage to get it on 90% sale. And for that money even if its short (in the end a good TD player probably could get all achievements in as short as maybe even 1 day) - its a really good and fun "classic" TD game - good replacement for any flash TDs.