• Diablo I - https://github.com/diasurgical/devilutionX
• Zelda: Link to the past - https://github.com/snesrev/zelda3
• Metroid II - https://flathub.org/apps/io.github.am2r_community_developers.AM2RLauncher
• Sonic 1/2 - https://github.com/Rubberduckycooly/Sonic-1-2-2013-Decompilation
• SonicCD - https://github.com/Rubberduckycooly/Sonic-CD-11-Decompilation
• GTA3/GTAVC - https://github.com/halpz/re3 (Original project github link not available)
• Papermario - https://github.com/pmret/papermario (US Rom 100% decompiled, but don't have a port yet)

If you use steam, this project https://github.com/luxtorpeda-dev/luxtorpeda, converts proprietary engines to use opensource versions when available. Here: https://luxtorpeda-dev.github.io is a list of games supported by this. How to use Luxtorpeda on Steamdeck: https://www.gamingonlinux.com/2022/03/steam-deck-using-luxtorpeda-for-morrowind-warzone-2100-and-x-com/

Not quite the same thing, but Project '06 is a ground-up fan remake of Sonic '06 in Unity engine that's actually fun to play

There's a number of games like that being reverse engineered, Majora's mask, minish cap, perfect dark, etc. But it's a pretty slow and long process. And until the game is reverse engineered and a 1:1 decompilation achieved, the ports like sm64 and soh aren't possible.

I’ve heard of a few but I honestly can’t recall I think maybe link to the past was decompiled. Maybe one of the sonic games.

I used to ai to the regames subreddit which was all about reverse engineering.