I've recently discovered and been playing through the Metroid Prime Trilogy after discovering PrimeHack which is a fork of the Dolphin Gamecube and Wii emulator that adds native mouse and keyboard controls to the Wii version of the game.

I realized that a lot of people probably aren't aware of the existence of stuff like this and was hoping to discover some more of these things myself as well as share the ones I'm aware of with the community.

Some other cool things I've run across:

Pikmin 1 & 2 mouse and keyboard control config for Dolphin

Portal: Reloaded - a Portal 2 mod (requires owning Portal 2 to download) that adds a 3rd time portal that allows you to travel between the present and the future

Starcraft: Mass Recall A complete Brood War remake in the SC2 engine. Completely free as only the free SC2 download is required to play.

Mario Kart Fun A mod for Mario Kart Wii that adds an absurd (400ish) number of custom tracks to Mario Kart Wii

Newer Super Mario Bros Wii A super mario bros wii mod that is a fan-sequel to the game with 128 new levels

OpenRCT2 is an engine re-implementation and enhancement for RCT1 and 2 that also adds features like multiplayer

OpenMW is an engine re-implementation and enhancement for Morrowind that adds a bunch of wild features

TES3MP is a fork of OpenMW focused on adding multiplayer support for Morrowind

Nitrox is a multiplayer-focused modification for Subnautica

DSP Nebula Mod is a multiplayer mod for Dyson Sphere Program

sm64pcBuilder2 is a program used to help you build the various pc port/modification efforts of the Super Mario 64 PC decompilation project

Ship of Harkinian is one of two PC ports for Ocarina of Time. They distribute tools to build through their discord which I don't love, but I linked their most recent video so you can find that info if you want it

Stardew Valley Expanded is one of the largest modifications for a game that I've ever seen. Check the page for a full list of additions