This is a list of mods I put together that make Starbound a much deeper game. There's plenty of content in vanilla for completion of the main story, but this gives you more to do during endgame. These mods increase the difficulty and learning curve of the game, but I have some suggestions to help with that. If you are new to Starbound, I recommend waiting until you complete the story to use these mods.

• Tanz Lighting Overhaul
  Great mod that gives every light source the ability to cast shadows. DO NOT USE UNLESS YOU HAVE A DECENT PC
  
• Xbawks Character Extender
  Required for Frackin' Universe and any other race mods you may like.
  
• Frackin' Universe
  A really good expansion beyond vanilla. THIS MOD WILL BREAK YOUR GAME IF YOU UNINSTALL IT!
  
• S.A.I.L. Customizable A.I.
  Goes with Frackin' Universe's S.A.I.L. modification
  
• Frackin' Music
  Adds a ton of ambient music to Starbound that couple with the new biomes from FU.
  
• Frackin' Universe - Melee Aiming
  Because aiming your weapon where you want to is necessary.
  
• Exended GUI
  Allows more items to fit in GUI windows, great for higher resolutions.
  
• FU + Extended GUI
  Makes Frackin' Universe work with this mod.
  
• More Planet Info
  Gives more information on planets and is fully compatible with FU's added planets and biomes.
  After June 2019 also subscribe to Quest Marker Fix and Lush Planet Fix for this mod.
  
• True Space
  Solar system spawning is made more realistic by having planets spawned closer to the star warmer and planets farther away colder, etc...
  
• RPG Growth
  Adds character progression on top of the myriad of crafting progression provided with FU.
  
• Planetary Clock
  Now you can see what time it is while on planet so you know how much day or night is left. Use with Stardust Core Lite.
  
• Stardust Core Lite
  Compatible with Frackin' Universe, RPG Growth, and Planetary Clock which will now show up next to your quick bar on the right of your screen.
  
• Food Stack
  Allows for stacking food up to 1000.

I chose not to use Frackin' Interface because it breaks other UI mods that provide more than just aesthetics. If you would rather use this, just don't subscribe to Extended GUI or Inventory Interface Redone. Last, but not least, Disabled Drop for Survival is a good option for players that haven't played Starbound before, or just want to make the game a little easier since some of these mods increase difficulty tremendously. I have tested these mods together for several hours with no issues and I will be on the hunt for more. Make sure you back up your universe and player files prior to installation of any mods. Please rate my collection, have fun and good luck!

I will update this list as mods become outdated or are replaced.