Shenmue 1
Shenmue 2 (Dreamcast and Original XBox version)
Soul Calibur
Soul Calibur 2
Dead or Alive 2
Dead or Alive 3
Red Dead Redemption
and there are many more

Wind Waker
Okami
Resident Evil Remake
Resident Evil 4
Super Smash Bros Melee
Metroid Prime 1 and 2
Super Mario Sunshine

Honestly, there's a plethora of 16-bit games that still (and will always) look fantastic.

It's the 5th (N64/PSX/Saturn) that certainly hasn't held up well, and to a lesser extent the 6th (GCN/PS2/Xbox) compared to what we see now-a-days.

For the 5th gen, it's ironically the 2D styled games that hold up best today. Castlevania: Symphony of the Night, Yoshi's Story, Suidoken, Paper Mario... while the more technically "impressive" games of that era (Ocarina of Time, Perfect Dark, Conker's Bad Fury Day) haven't aged nearly as well from a graphical standpoint.

The 6th gen holds up much nicer, and there's certainly a lot of games that "look nice" to this day. However, there's only a few that can still hold their own against today's graphical juggernauts, and that's only because of their creative art directions that used the power behind the console in creative ways. Viewtiful Joe, Okami, The Wind Waker... these are some games that can be played by anyone today and not lose a beat (well, there's always a lack of widescreen, but other than that...).

I tend to agree. 2D ages better than 3D in general. I see this continuing even with the 7th gen; I'm confident that long after games like The Last of Us and Halo 4 have fallen behind the curve, games like Rayman Origins, Kirby's Epic Yarn, and Muramasa will still look gorgeous.

Also, 5th gen 2D games don't get enough credit I reckon, as you pointed out there are some really handsome ones.

I'm big on art style when it comes to games. Jet Set Radio still looks good to me because of its style, even though it's an early 6th gen game. I'm a sucker for the cartoony Jak and Daxter art style too. I also really liked the visuals on some other 6th gen games such as Metal Gear Solid 3: Snake Eater and GT4. The Soviet jungle/Groznyj Grad in MGS3 still holds up pretty well for me, and not just in the HD version of it.

My most recent playthroughs include Resident Evil (GC), Super Mario Sunshine, and God of War 2. All three looked fantastic and have aged well if you ask me.

This. The 5th gen looks terrible to me now, and this is sad because I grew up with that generation of game. Games like Super Mario 64, Super Smash Bros, Mario Kart 64, GoldenEye 007 all feel dated to me because of the early 3D graphics in those games. However, SNES games seem to run like a dream, the sprites look nice and the games run smoothly. I whine like a little bitch when playing Super Mario 64, but I don't whine when playing Super Mario World or a 2D 5th gen game such as Paper Mario, as you just mentioned.

Sure! Just let me grab my nostalgia glasses...

Dragon's Lair forever.

It's not just nostalgia, as it applies to games I didn't play until recently too.

I don't have to have played it as a child to find this beautiful:

on emulator yes there are Plenty, pretty much every SE (Except FF7), KotoR, Nintendo game, and RE4. On CRT they still look great as well.

on an LCD using an original console is ugly low res jaggy for me and I can't do it. luckily I don't have to, I have CRT or I just emulate it if I can get it working.