I think Half-Life 2 in 1600x1200 with 8xAA and 16xAF, everything maxed out looks pretty stunning using that texture replacement mod (something with cinematic, can't remember the name right now). Its not one thing that looks superior in that game (like in Doom3 where character models looks stunning). In HL2 it is the overall quality that is great!
Other than that, well Prey looks pretty good too. F.E.A.R is also looking great.
so my list would be:
1. Half-Life 2 (with cinematic texture pack)
2. F.E.A.R
3. Prey
4. Doom3
5. Far Cry (was really impressive when released and still looks kinda good)
There you go..