I love the fact that nobody voted for Far Cry 2.
I say Far Cry 3, having played only the main series games.
Far Cry is an enjoyable and highly challenging game with some great environment and level design and shooting. I actually prefer it to fellow 2004 FPS Half-Life 2. But it's too unforgiving for me, and it's very linear by design. Still, a great game.
Far Cry 2 is a poorly designed mess. The setting is nowhere near as interesting, the world is overly confusing, you are killed wherever you go by enormous armies of enemy mercenaries. It's a very, very frustrating game.
Far Cry 3 is one of my favourite games of the year. It almost goes to the opposite extreme and becomes too easy: I agree with TotalBiscuit when he says that Jason being Rambo is a little bit disappointing, the shooting should perhaps be a little harder, and there should be some survivalism built in. But it's a huge and beautiful world (with hang gliders!) filled with side missions, with a great story and characters, and a hunting mechanic that is actually important and enjoyable (looking at you, AC3). I'm far from completing it, but I think it's by far the best of the three.
(Former) Lead Moderator and (Eternal) VGC Detective 
