Things that held up well:
Zelda Wind Waker - Honestly an amazing game to me. I wouldn't say it's perfect but it comes damn near pretty close to perfect. Can't really complain about much, other than a few of the late game objectives were ehh. Makes me sad to hear it got so much backlash when it first came out though. I think tards were just pissy about the Cel-shaded cartoon graphics, but those have aged like a fine wine and look beautiful even today.
The Timesplitters series of games is another example of something that has held up very well for me. Great humor, awesome music, and a surprisingly good story for the third one. There is an insane amount of variety even for the time. The amount of content and things to do in those games is wild compared to anything that comes out today. I spent probably 2000 hours on the Mapmaker.
Things that HAVE NOT held up well:
The Sonic Adventure series of games. I fucking loved these as a kid. Played them for hours on end each day just grinding the chao gardens and replaying the levels from the story once you finished it. Thought it was the most epic shit ever.
Replaying them as an adult though? Yeah they're fucking bad. Awful camera system, shit voice acting, nonsensical storyline. Any of the Non-Sonic stages are flat out unfun to play through, the gameplay for Eggman, Tails and Knuckles are just poopy watered down versions of better games in the industry at the time. The music is a hit or miss. Some of it is pretty good, some of the other ones are just embarrassing. I replayed Adventure 2 for as an adult for like 3 hours and was like, yyyeeeahhh, this is not good. Never touched it again. The First Sonic Adventure holds up better, though it's also still pretty mediocre.
The first two Halo games have also not aged particularly well in my opinion. The story in Combat Evolved is really bland, and the second half of the game is just a fucking DRAG to play though. Copy and pasted levels, bullshit enemy types. The thematical reveal for the flood was excellent, as is the music. But, it's just a very dated game. Halo 2 holds up even poorer IMO. You can really feel the development hell playing through it. The harder difficulties are unbalanced as fuck, and there's a lot of leftover content from cut features in the game, which break the overall experience. The story is also dated and you can really feel it was made during that 2004, War on Terror patriotism during the Bush era.
Halo 3 was a masterpiece in every regard though. Completely superior to the first two games. Story and gameplay improved leagues above them. Reach was great as well. The first two ones are just not worth going back to IMO.