How did I miss this?
Perfect Dark at #55 is a disgrace.
Deus Ex and Metroid Prime aren't shooters, although they are masterworks.
Half-Life is a solid choice for #1, although I think its sequel is superior.
My own top 5:
5) GoldenEye 007
4) BioShock
3) Perfect Dark
2) Half-Life 2
1) Halo: Combat Evolved