A few I can think off the top of my head:
Marvel Vs Capcom 3 EX: Fixes some bugs, QoL changes such as every character can link standing and crouching normal attacks like most of the cast (crouching Medium into Standing Medium for example), bad bugs fixed, and changing some assists for characters, including some that are just plain awful like Deadpool's Trigger Happy attack now being the Medium version (which shoots straight as he stands upright) instead of his heavy (meant to be an anti air shooting diagonally.)
Sonic Genesis Done Right: A romhack of Sonic Genesis, or, Sonic the Hedgehog on the Gameboy Advance, that showcases that the game could be handled ported. Sonic Genesis is an extremely awful port with slowdown, bad screencrunch, and an extremely bad redone soundtrack on the GBA soundchip. This mod fixes almost all of that. And to think, a decade later, the person who made this would go on to make Sonic Mania.
Literallly most Payday 2 Mods: Payday 2 is a great game but holy hell does it need some QoL improvements. Tons of mods make it an even better experience, including my favorite thing that's yet to be implemented, Toggle Interaction. Some interactable items can take almost a minute to fully interact.
Honorable mentions:
Street Fighter 4 Remix: A more interesting experience. Pretty much Street Fighter II Rainbow Edition for SF4.
Pokemon Romhacks: Depending on the kind, the best ones are the ones that let you obtain/evolve Pokemon you normally couldn't during emulation or in a single player experience.
Brawl Mods: Project M is usually the first to come up, but I personally love Brawl Minus, a game that was taking the piss out of multiple mods trying to "balance the game" with obvious bias, but the real goal was to make the game a chaotic broken mess.