Galaxy is in a class of its own. COD4, Prime 3, Bioshock, and Portal would be GOTY in many other years. Though Portal being so short does hurt it. Halo 3 is also the only game in the franchise that I think lives up to the hype built around the franchise. 1 and 2 I found to be meh games, but 3 was actually really good.
For me, its
1 Galaxy
2. Prime 3 (Resident Evil 4 Wii edition would go right after it if it was a new game and not a port of a 2005 game)
3, Bioshock
4. Portal
5, COD4