I think all three are worth playing. I thought Clear Sky was the weakest of the three, mostly because it never makes that much use of some of its more interesting features (faction war etc.), came out a bit more buggy, and of all the games is the quickest to force you down a linear kind of endgame path. Try as they might, S.T.A.L.K.E.R. games were always the weakest in their linear parts (except maybe the X-labs which were and always will be scary as heck), and best in the open world. My best experience with the game by far has been in the Misery mod for CoP, though even I'll be first to admit that it's not everyone's cup of tea and is possibly too hardcore. Then again, you could say that about S.T.A.L.K.E.R. in general - it's not something that works for everybody.
Otherwise, I think it's a testament to the game's strength and concept that after so many years there is still an active, loyal and shamelessly hardcore following for it, and mods are still being made and improved. I think one of the draws of the game is that it's really pretty uncompromising and pretends that the last decade or so of 1st person shooters never happened. It's mercilessly hard, and it tells you nothing. There's no "run here! shoot this! HEADSHOT! achievement unlocked!" and it always explains very little about the zone, how it works, who your enemies are, or how to beat them. It doesn't tell you where the entertainment is, and in fact, does nothing to promise you fun. The zone runs by its own rules, but it's not going to tell you those. When it tries to explain, it does so kind of poorly, but in a way that actually makes it better because it keeps you in suspense. You're left to make sense of it and survive on your own, and it's really easy to screw up. Almost any time that you squeeze the trigger in S.T.A.L.K.E.R., you don't really know what's gonna happen. The gunfights in it are a million times more interesting than in any "modern" single-player shooter. The game world is more merciless and more immersive. And I think that's what keeps a certain group of players always coming back for more
