Playstation 3: The Last Of Us

Xbox 360: Halo 4

Xbox 360 & PS3: Alien : Isolation (even if the stability is not optimal)

Xbox One FAT & PS4 FAT: Red Dead Redemption 2

Metroid Prime - I'm surprised this hasn't been said yet. A technical marvel. The remaster has some saying the same thing today.

Kingdom Hearts - The prerendered cutscenes at the start and end of this game blew my mind. I didn't think things could look so amazing on a PS2.

Metal Gear Solid 4 - I remember my brother and I having a "MGS4 standard" when it came to graphics in games. In 2008, there wasn't anything that I knew of on it's level.

Pikmin 3 - Never played it but every screenshot I saw I thought it had to be PC renders. Just a crazy looking game.

Xenoblade Chronicles X - Just ridiculous. The scale and moving parts and rendering, I really thought this wasn't possible.

Speaking of PS3/360, the port of Crysis to those systems was one of those things that sounded impossible until it actually happened.

Yeah, it didn't run that well, and the graphics were downgraded, but given the game's mythical status as the ultimate high end PC game that consoles could never dream of running, the fact it functioned at all felt somewhat miraculous.

I'll give a shoutout to MGS5 on PS3/360 as well for pulling off an 8th gen physically based lighting model on 2005/2006 hardware, in an open world game no less. Again, performance wasn't great, but that's forgivable given it was pushing way more than the hardware was ever designed for.

The DS had a few. 

Moon 

The Wizard of Oz: Beyond the Yellow Brick Road 

Phantasy Star 0 

All of these games, when upscaled in an emulator look almost Dreamcast-like/lower-end 6th gen titles. For example, here is TWoZ being played at 4k. Look at the water at 9:08. 

and Moon at 4k. 

Gives original half-life vibes. 

Some that come to mind:
DOOM 3 and Half-Life 2 on PC looked better than any console game pre-2007, absolutely ridiculous that they both made it to the og Xbox, looking and playing well.
The Xbox 360 also had some insane ones like Halo 4 and Rise of the Tomb Raider, which some argue is superior to the Xbox One version. MGSV on PS3/X360 also come to mind.

Virtua Fighter 2 on Saturn is also crazy, 708x480 resolution, 60 FPS, would have been impossible on PS1 or N64. Panzer Dragoon Zwei and Sega Rally Championships are other extremely impressive Saturn games.

I remember being quite stunned by Mario Kart DS.

The Switch is of course the champion of impossible games, The Witcher 3, Doom 2016, Doom Eternal, Hellblade: Senua's Sacrifice, Dying Light.

The Wii U got Xenoblade Chronicles X, Breath of the Wild and Paper Mario Color Splash.

Alien Vs Predator on the Jaguar is also impressive, truly looked like a fifth gen game.

That Wizard of Oz looks incredible for a DS game, holy cow.  Looks like a lower budget 3DS game, really fascinating. 

It's been a while since I played it, but I remember The Conduit 2 having some sick graphics for a Wii game

Yep, I'd say it even looks almost as good as some first/second party 3DS games, like Pokemon X/Y. 

vs. 

Both are upscaled using emulators.