A hard question; I'm a pretty big fan of the Witcher series. Maybe cause I'm Slavic and like the mythology, or because I'm very lenient about flaws if a game has other original or redeeming aspects.
W1 was amazing at the time, with excellent atmosphere (perhaps helped by the stilted dialogues), moral ambiguity masterfully done, and a very cool story. C&C was very nice as well, as was the way you had to figure out stuff for yourself - you could fail a great detective portion of the main quest, for god's sake. Before it came out I was resigned I'd never again play a new real RPG other than perhaps some indy stuff. Combat was shit, etc. etc., but so what?
However, looking back on it now, I have to say I dislike how the game had obviously evil antagonists. For all its moral ambiguity in the side stuff (including the huge and excellently done terrorists vs. fanatics dilemma) you never had any doubt you were doing the right thing in the main quest. For this reason alone, I can't give it the top spot in comparison with the others.
W2 broke new ground in a spectacular fashion. I mean, it was very very flawed, but the sheer ambition of the game was shocking to me -
every other developer would have stuck with the formula that worked in the previous game. And that's why I like the Witcher games: each one break new ground, and despite the flaws at the end of each I think "Damn. I'm never gonna play a game like this again."
Through amazing effort, W2 had:
Even worse combat than the original.
A fucking split down the middle of the story where your choice completely changes your path through the game. Fuck me.
Great political intrigue, and a very nice taste of why Geralt detests it and has his questionable philosophy of neutrality. Another minor flaw of the first game for me is that the injustice (against the nonhumans, of the terrorists killing innocents) is immediate and combatable directly, white-knight style. W2 shows how many political factions pulling in various directions can make clear good deeds have bad consequences. Better to stay the fuck out of it and just do your job, says Geralt, and I start to understand his view.
Also, there was
no clear evil antagonist. At worst, the various factions could be seen as ambitious and/or imperialistic. And the main bad guy - you get to walk away without fighting, if you want to. Damn.
For an excellent analysis of the realistic politics of W2, I really recommend these articles:
http://knightofphoenix.tumblr.com/witcher
W3 had the best open world I remember after Gothic. Fuck me! Sure console bullshit crept in and much of the potentially great detective stuff ended up railroaded, but yeah, I haven't had that open world feeling since the heyday of the Gothic series. This is high praise, but also had a effect along the lines of being lost in the political intrigue in W2 - in W3 I started off white-knighting through my quests in similar style to W1. But the world is so large, the scale of the suffering and terror of a war between nations well shown, that after the nth burned village you go through with people hanging from trees (and no quests! just a village), I just started feeling numb to the horror. I started to approach sidequests with a "I'll just do my job and you sort out the rest" mentality, and towards the very end my general feeling was "fuck this shit, I don't care what happens globally just want to save the people I care about". Which, again, is Geralt's philosophy, pretty much.
And although Ciri is a Mary Sue, sorta, I think this was a father-daughter relationship done well, especially in the sense that the daughter is grown up and, arguably, way more competent and powerful than the father. Not many of these stories done well around. Was reminded of Les Miserables a bit. But the main storyline suffered somewhat from the abitious scope of the game - some things could have been more fleshed out. Really liked the Yennefer character though, who I was skeptical about at the end of W2. Also there were at least two scenes I found a bit touching, which is not really something present in previous Ws.
Another thing I liked was how many of the final consequences were aggregates of the way you built up the relationships with others during the game, not single tipping points.
And of course, the fact that the game has 100+ quests and
not a single fetch quest - they all have a neat little story and often a pretty good twist to them, even bullshit "kill a monster" ones - is incredibly impressive.
So TL:DR: They are all good though flawed games, each one with some impressive ambitious feature. For me, it's a tossup between W2 and W3. Again, I recommend the link I gave for great insights into W2.