A MegaCollection Kit

Please let me know of anything else I could add in the comments at the bottom.

There are too many mods to list so I will not be listing them all, save for a few Adventure/Modern mods. For some recommendations, the Perfect System Guidebook (PDF hosted on Google Drive) has a good amount. Almost all mods for every game can be found on GameBanana. Some mods and romhacks are hosted on the Sonic Hacking Contest vault. SHC also lists the mod loaders for all other games and further decompilation guides. Sonic Retro hosts some romhacks too, as does Romhacking.net. Note that the Genesis/MD romhacks on Sonic Retro and Sonic Hacking Contest tend to be prepatched ROMs.

Classic

Sonic 1, 2, 3 & Knuckles, CD, Mania

To mod Sonic Origins, see Hedge Mod Manager below.

Decompilations

Based on the 2013 phone ports of 1 and 2, and the 2011 phone/PC port of CD. Grants enhanced mod support compared to the originals, and can be ported to Android and other platforms. Add script decompilations to access more mods. Has partial support for the Sonic Origins versions. Requires original files. Either the .apk files of the Android ports, or a Data.rsdk file pre-extracted from the games or found in the CD 2011 PC port or Mania will work. Origins files will work with limited support, but it's recommended to use those with the v5U decomp. DLC content (Mania Plus, Amy and Knuckles when using Origins Plus as a base) will be locked unless the decomps are built from source.

• Sonic 1 and 2 (Retro Engine V4) (Script Decompilations) (Script Decompilations)
• Sonic CD (Retro Engine v3)
• Sonic Mania (Retro Engine v5/v5Ultimate)

For managing mods, one-click installs, and auto updates, use RSDK Mod Manager. Maniatic Launcher can be used for the Mania decomp. Cosmic Engine is a WIP source port/rewrite of the Sonic CD engine (Retro Engine v3).

Sonic 3 A.I.R. - Angel Island Revisited

Official Site, Forums

A separate port of Sonic 3&K. Requires the ROM from the original Steam release. Also has Android and Flatpak (Linux) versions. Mods can also be found on the forums.

Team Forever Versions: Sonic 1 Forever and Sonic 2 Absolute

Website

Basically special versions of the decomps with their own features. They have their own mods (see GameBanana) that can be managed with RSDK Mod Manager (see above). For an equivalent for Sonic CD, see Sonic CD Restored or Miracle Edition.

Adventure/Modern

SADX Mod Loader and SA2 Mod Loader for managing mods for the Steam ports. Reloaded II for Sonic Heroes, NiGHTS into Dreams..., and more. Hedge Mod Manager for the Hedgehog Engine games.

For some of the more notable mods, Render Fix clans up some graphical mistakes for SA2, while Chao World Extended and Enhanced Chao World can work together to add so much more to the Chao Garden. SA2 Good Edition removes all non-Sonic/Shadow levels, great for quick replays. The SA1 Mod Manager will install Dreamcast graphics restorations by default. For Generations, the Unleashed Project, a port of the Unleashed day stages, and the Direct3D 11 mod upgrades the graphics API to improve performance.

Emulation

Some links here are copied from EmuKit.

Sonic 2 Community's Cut is a combined romhack and custom version of Genesis Plus GX to add extra features like widescreen, if you have the original ROM. Sonic 3 Complete is a hack that adds improvements to the original game that stay faithful to the original Sonic 3, and the version you get can be customized from the website. Sonic 3D Blast Director's Cut is an improvement patch made by one of the original devs, and can even be used within the Steam version through Steam Workshop. Sonic 3 & Knuckles - Battle Race is another hack.

For the 3D games, Shadow The Hedgehog: Reloaded in an improvement mod for the GameCube version, Legacy of Solaris (GameBanana) improves the 360 version of 2006, and Sonic Colors DX is a Dolphin fork for playing Colors in HD, and optionally restore the level order. The DLC Restoration mod for Lost World adds the Yoshi and Zelda levels from the Wii U version back into Lost World for PC. Extreme Gear Labs host Sonic Riders DX and Sonic Riders Regravitified, competitive mods for the GC and Wii games. Sonic Riders Tournament Edition is an alternative. The No Kinect Patch adds controller support to Free Riders.

Fangames

2D

• Sonic and the Fallen Star: Well animated.
• Sonic Triple Trouble 16-Bit: Remake of the Game Gear game. (Game Jolt)
• Sonic Time Twisted: Sonic CD sequel. (Game Jolt) (Itch.io, with Android version)
• Sonic 3D in 2D (Itch.io): Sonic 3D Blast reimagined as a 2D game.
• Sonic SMS Remakes: Remakes of the Master System games with new characters and modes, and an original game too.
• pico sonic: A bit of Sonic 3 in PICO-8.
• Sonic Mini: Sonic on TIC80.
• Sonic 2 HD: Remake of Sonic 2 with high quality art. Unfinished.

3D

• Sonic GT (Game Jolt): Short 3D game.
• Project 2006 (YouTube, see description for download links): Remake and drastic improvement of Sonic 2006.

Other

• Sonic Battle R: Online racing game. (Game Jolt)
• Sonic Runners Revival: Revival of the phone games.
• Sonic Runners Reloaded (Game Jolt): Remakes of the above.
• Sonic McOrigins Plus/LCDonald (Github) (Itch.io): Simulators for the McDonald CLD games.
• Sonic Smackdown (Itch.io): Fighting game that's basically Marvel VS Capcom 3.
• Chao Resort Island: Standalone Chao garden.
• Sonic Boll: Mario-styled Sonic crossover platformer. Moddable (Gamebanana).

Also see Sonic Robo Blast 2.

Resources

• Mania decomp building guide (GameBanana)
• Guide to install every Sonic game onto Steam Deck (Google Doc)

YouTube

• Video version of the instructions for building decompilations from source
• Helpful guide for getting into the right mindset when actually playing the classic games

Background taken from here.

Suggest more in the comments!