Hmm... well, I wasn't a big FPS gamer before 7th gen started (I only played CS 1.6 a lot^^), so my list will only/mostly contain 7th gen FPSs:
1. Killzone 2
2. Bioshock
3. CoD: Modern Warfare 2
4. CoD: Modern Warfare
5. Bioshock 2
6. Resistance
7. Resistance 2
8. CoD: World at War
9. Half-Life 2
10. Battlefield: Bad Company
#3 - #7 could also be a bit different in order.
2012 - Top 3 [so far]
#1 #2 #3