I'd put Half Life 2 in there, not only did it improve on the first game by a huge margin but it had a massive influence on the whole genre. A truly amazing sequel.
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Which makes the wait for the next one so painful.
2. Portal 2
3. Team Fortress 2
No seriously, the original games came out so long before the sequels that the sequels end up being way different and better games.
Left 4 Dead 2 Though? Nope.
Edit: It's actually a prequel, but it's so good I'll leave it here anyway.