Kurokami said:
Almost all of them.
Really? You prefer sequels?
Doom II is better than Doom.
Unreal Tournament 2004 is better than Unreal Tournament.
Feeding Frenzy 2 is better than Feeding Frenzy.
Geometry Wars 2 is better than Geometry Wars.
Gran Turismo 2 is better than Gran Turismo.
Super Mario Bros 3 is better than Super Mario Bros (2 doesn't count, it's Doki Doki Panic).
Quake 2 is better than Quake.
Descent 2 is better than Descent.
Civilization IV is better than Civilization III (Civilization 2-3 was an odd switch where it wasn't better or worse as much as different).
Street Fighter II is better than Street Fighter.
Gears of War 2 is better than Gears of War.
Grand Theft Auto 2 is better than Grand Theft Auto.
Soul Calibur is better than Soul Blade.
WarCraft 2 is better than WarCraft.
Windows 7 Minesweeper is better than the previous iteration that existed since 3.1 through Vista.
I could go on.
The closest thing to an exception I could see is Burnout Takedown & Revenge to Paradise City, where I don't like it because it's a different game, rather than a subsequent game actually being worse.