What are we talking about? The graphics of the games or the graphical potential of their engines?
Games...HL2 has the best graphics.
Engine...Doom 3. Technically it can be considered better than Source but Source as an overall engine is better.
But HL2/Source is still the most realistic graphics I have ever seen in a game. Doom 3 looks fake and the models look like plastic dolls. The scalability of Source is incredible.
Far Cry's graphics are really good but I like to see how Might and Magic will use Source and how it renders "fantasy" outdoor environments. I still think Source can render outdoor environments better and more realistically than Cry Engine 1. But Far Cry's outdoor environment looked better than HL2 mainly because of where the games took place rather than what the engines can do.