I don't think any of the early FPSes really qualify-- though they were the first, they can't come anywhere close to the polish and playability of modern FPSes.
Anyway, Portal.
Quake 3 was the best Quake-- UT99 was the best UT. Halo 1 was the best Halo, and pretty much defined all future console FPSes. Starcraft is by far the best RTS in that it has a large following, and with good reason. I can't say anything about MMOs, though.