It has to be Assassins Creed 2 and Uncharted 2.

With ACII, the franchise went from being a 6.5/10 game to 9.5/10 and is still the best the series has seen. Everything about ACII was perfect, from the setting to the story and the gameplay. Even the characters were more likable this time round.

With Uncharted 2, they just upped the ante. The first one is still decent (7.5/10 imo), but Uncharted 2 blew it out of the water. The set pieces and level design were top notch.

Super metroid: Going from "good" to "one of the best games ever made" is quite the feat.

Warcraft 3 (as a sequel to Warcraft 2)
Command & Conquer Tiberian Sun (As a sequel to C&C)

Mass effect to mass effect 2

Uncharted to uncharted 2
Uncharted 3 to uncharted 4

Mk 9 to Mk X as I despised 9.

Dragonball Budokai Tenkaichi 2
Tekken 5
Assassin's Creed 2
Uncharted 2
The Witcher 3
Grand Theft Auto 3

Uncharted 2
GTA 3 and 5
GT2
TimeSplitters 2
Super Mario World and Galaxy
Halo 3
Assassin's Creed 2
Panzer Dragoon Saga
Shining Force 3
Zelda: A Link To The Past

I'm sure there's more but I'm drawing a bit of a blank beyond those.

-Wind Waker (it has combo).
-Half-Life 2 (physics).
-San Andreas (bigger map).
-Halo 2 (more polygons).
-Metal Gear Solid 2 (improved cinematic).
-Doom 3 (improved graphically).
-Metroid Prime 2.
-Pokemon Gold/Silver (two freaking regions)

Edit: And of course, Super Smash Bros. Melee (Faster paced)

- TMNT 2 The Arcade Game
- Street Fighter 2
- Uncharted 2
- Killzone 2
- Half Life 2
- Legend of Zelda A Link to the past
- Final Fantasy 7 ...that's right I said it! =P
- Resident Evil 5 ...that's right I said it again! =P

That pains my soul.

For me:

Mass Effect 2

Uncharted 2

Killzone 2

Link to the Past

Assassins Creed 2

Arkham City

Metal Gear Solid 2 improved on every single aspect of the original. The ability to actually shoot from behind cover, the implementation of walking/running, a first-person aiming mechanic that the original sorely lacked(most likely due to technical limitations of the hardware), holding up guards, shooting out radios, the ability to go through the whole game without killing anyone, collecting dog tags etc. I could go on and on.

Perfect Dark took everything that made Goldeneye amazing and amplified it. Better graphics, more weapons, alternate firing modes on every single weapon(even melee), more complex and involved missions, more intricate levels, feature packed multiplayer, AI controlled bots, counter-operative mode, co-operative mode, certain levels from Goldeneye included for multiplayer, smarter enemies who would call for back up and/or pull out pistols when you disarmed them. Amazing.

Killzone 2 massively improved on the original, as did Gran Turismo 2 and GTA3.

Ocarina of Time/Super Mario 64 deserve huge mentions if they are considered true 'sequels' to their SNES predecessors as both were hugely revolutionary.