Some mods obviously won't work with Rising Stars. Others might have some quirks that need mentioning, and others still won't work because they've already been included in the mod. The game does typically tell you exactly why things won't work, but I guess a centralized list could help.

So, here's a list compiled in response to Viking.exe's comment #291:

• Pure shipset mods should work. So long as their stuff is self-contained (not messing around with other subsystems like FlagshipHull), it'll work, which means that everything from DOF's shipsets to my Protoss shipset will have no problems whatsoever. Unless we're using the same namespaces, in which case a bug report is needed to solve the problem in the next patch.
  
• Flag and race portraits will work, under the same restrictions as shipsets. Vincent's Terran Race mod will not work, nor will anything that modifies the harrian.png portrait or contains SR1 portraits.
  
• Music mods should work. My 'Multiple Theme Enabler' script, however, will not work as it has been integrated into the mod.
  
• Gameplay mods of any kind should ideally be avoided altogether for balance reasons, but there's no simple rule that says 'this works, that doesn't'. The mod's just too broad to make a simple ruleset. Scripts are equally difficult to classify, and compatibility can be broken at any time.

NOTE: Some or all of these mods might not even work in the vanilla game. Those mods definitely won't work with Rising Stars, even if this list says they're compatible.

• Alternative Interface will not work. However, Vaaish has put out a special variant of AI that will work if you disable RS itself. To use RS without AI, just disable AI and reenable RS.
  
• GovMod should work. You might not get a Capital if you're playing Ringworlder Vanguards (Bluuhbi, not currently in the mod), though.
  
• DOF won't, for obvious reasons. Its shipsets are okay, but the actual 'code mod' is thoroughly incompatible with Rising Stars.
  
• Darloth's Subsystem Assortment won't work because Rising Stars contains some of that and discards the rest.
  
• Similarly, while Building Assortment might work now, ABEM used to modify the Ancient Planetary Defense and now that Darloth's onboard he may make other modifications too.
  
• Reclusive Ringworlders were also in ABEM in a modified form, so that is/will be gone.
  
• However, Hive should work.
  
• Governmental Rebalance will probably work.
  
• I occasionally see people running the Weaponsmith-RS combination, so that works. It's also the least likely to cause balance issues, from what I know of it.
  
• MD Wolfes Governance Mod probably won't work, its scope is greater than that of GovMod by a significant margin.
  
• No Station Upkeep shouldn't work, Faster Turning probably won't work. Resource Producer might work. Crazy Subsystems should work.
  
• Flak Cannons for Flagships will probably work now that ABEM's Flak Cannon is a thing of the past.
  
• Astronomical Names and WWII Ship Names ought to work.
  
• More Weapon Colors will break horribly.
  
• Bigger Astronomicals might work.
  
• Prewarp won't work.
  
• Technological Rediscovery and Diverse Hull Types won't work (not sure if they even work with vanilla SR2 anymore), nor will No Maintenance.
  
• Advanced Pirates might work, if it still works with vanilla. Given that its author disappeared before 1.0.2 was released, this is questionable.
  
• Aqua Races Addon might work.
  
• The 'MEM Mega Economy Mod' probably won't work.
  
• No Gaps For Artificial Planetoids might work, Economic Sanctions probably won't work anymore.
  
• Large Game Customizations won't work, nor will FTL Research.
  
• Strange New Worlds used to work and probably still does.
  
• Handicap Mod is integrated into RS, so it won't work.
  
• Standard Forge might work.
  
• Economic Overhaul and Mobile Construction won't work.
  
• Removable Buildings might work, but it might not.
  
• Station Love probably won't work, Shield Rebalance won't work.
  
• CheatBoost Govs should work, Asteroid Capture might work.
  
• No ABEM variant will work due to being out of date. :P
  
• Star Saga probably doesn't even work with vanilla anymore, let alone us. Same goes for BunkerCore.
  
• Silly Resources probably will work.
  
• Modular Fleet Systems probably won't work.
  
• Laser Mod won't work.
  
• Hangfire's New AI Races should work.
  
• The unofficial 'Alternate Balance Trait Expansion Mod' by dreadxx will work. Allegedly.
  
• Better Economy shouldn't work.
  
• Dragoon's Cheat/Sandbox Mod probably won't work.
  
• For your inner modder, Editor Expansion has probably gone the way of the dodo because Alar's been hooking up editor changes directly into the base mod.
  
• Devout Shrines might work?
  
• Super Crew Control System & Trade Station won't work.
  
• A Space Odyssey probably won't work.
  
• Null Mass Field might work.
  
• No Food or Drink... might actually work? Probably not.
  
• Mothership Size Determines Population might work.
  
• Populated Civilizations probably won't work.
  
• No idea about Rename Mod.
  
• Linear Rebalance won't work. I think.
  
• Food and Water probably won't work.
  
• Forges Shrink might work.
  
• Ran8's Simple Econ won't work.
  
• Orbital Mechanoid might work.
  
• Transport Ore doesn't even have a purpose anymore, as Darloth points out.
  
• Green Stars might work?
  
• Mothership Mod might work.
  
• Better Economy and Resource Management probably won't work.
  
• Diplomacy Tweak probably won't work.
  
• Post-Apocalypse lifestyle might work.
  
• Not sure if Personal Mod even works with the base game anymore, probably not. Same for Dereknor's Persistence mod.
  
• No Default Auto Fill won't work, unfortunately.
  
• Oceanic Space might work, but it probably won't.
  
• No Random Selection Boosts probably will work.
  
• Ringworld Research probably won't work.
  
• Accelerated Gameplay's vanilla compatibility is questioned by its author, its RS compatibility is doubly questioned by me.
  
• No Command Points probably won't work.
  
• Gerontocracy Government is... too vague to tell, but probably works.
  
• Human+ should work.
  
• SCIENCE x10 shouldn't work.
  
• Lazy Mechanoid probably won't work.
  
• Heretics might work.
  
• Versus Mod probably won't work.
  
• Metallic might work.
  
• AutoIRC is integrated into Rising Stars, I wish somebody actually used it.