Rocket Knight Adventures is still one of the best 2D platforming experiences you can have, imo. It's very short but it has a nice visual style, great music and sound (especially for a Mega Drive game), fantastic controls, a challenging but fair difficulty level and great level design. Well worth seeking out if you've never played it.
I think the Mega Drive Sonic games have aged really well, too. A lot of people don't like the momentum driven movement that means you can hardly jump forward from a standstill but if you dislike that now, you probably would have if it were still the 90s as well. That momentum based movement is precisely why I think they're good, nothing besides Freedom Planet really does that. And Freedom Planet, good as it is, messes it up a little in a few ways (there's never any reason to use horizontal bounce pads because you'll immediately come to a screeching halt after you hit them).
Someone mentioned A Link to the Past so I'll also nominate Soleil for the Mega Drive which is probably ALTTP's best clone besides Alundra on PS1, which has also aged extremely well and is, for my money, actually much better ALTTP in just about every way.
Team Buddies on PS1 was this weird little top down, team based shooter that is and was fantastic and there's just nothing else like it. It's rare as rocking horse shit now, sadly, but fuck me it's good.
Psi-Ops was a multiplat TPS from 2003 that had a pretty decent pre-Gears cover system, impressive AI and probably the best use of telekinesis in a game to date... to the point that you can fuck the shooting and cover system off and throw your enemies around like screaming ragdolls. Second Sight is also good. It's more stealth based and story driven but also has a surprisingly good cover system, great use of TK and other powers, a decent narrative and a distinct, very Timesplitters-y visual style. It suffers from some control issues that were a problem even at the time, though.
Speaking of Timesplitters, 2 and Future Perfect have aged really well for 6th gen shooters. Still my go-to for local multiplayer when I'm entertaining.
Pretty much any JRPG after the 80s that was good when it came out is still at least enjoyable today if you're into the genre but I have to give special mention to Shin Megami Tensei: Nocturne/Lucifer's Call for still having never been topped in my opinion. It holds up really nicely visually, too.