Either mods that remove annoyances from good games without altering the gameplay (so most of these could be recommended if you're playing for the first time, you don't have to worry about it changing the intended experience), or that try to salvage a bad game by making some gameplay improvements (pretty much only in the case of Mega Man X3, X5, and X6). Also including open source decompilations and PC ports. Not meant for anything that introduces original content.
If there's anything I missed here the best places to check for yourself are Romhacking.net and the PCGamingWiki.