Having played all three (okay, like half an hour of Clear Sky, never made it out of the swamp), it's really hard to pick one. In the poll I gave the edge to Call Of Pripyat, for its depth and much cooler anomalies, but the truth is both of the main ones were amazing, and some of the few games to absolutely scare the hell out of me. The labs especially, and the pack of wild dogs hanging out in the middle of Pripyat in CoP.
They're also notable for being really, really good with gun stuff (I think even the base versions, I played with the Complete mods). I once tested the HUD reticle rangefinder (engine-side, displays distance to what you're aiming at next to your crosshair) against the ranging tool on the PSO rifle scope, and it lined up really well. I think the drop compensating marks were even pretty close on.