Difficult question, because I liked them all. I think I'd have to say WC4.
For me it breaks down like this... I tend to like storytelling first, gameplay second, and pretty flashies (graphics, etc) last.
WC1 was of course the game that started it all...but like many "origination games" it was surpassed by it's sequels (if a sequel isn't better than the original, or at least as good, it's essentially a failure as a sequel=).
I liked WC2 because of the epic-ness of its storytelling, and it's attempt to go beyond the "fly mission, get debriefing, fly next mission" cycle. But I thought the gameplay was actually poor...It was essentially the WC1 engine, with some slightly prettier and smoother graphics...but somehow the smoother graphics made it feel more like a toy. I could forgive the pixelated WC1 graphics as "outdated", but WC2 still had the same outdated non-polygon engine, but actually looking better. Add to that the fact that I think they missed the boat on the capship combat mechanic, and I didn't enjoy the gameplay all that much. I essentially liked it only for the story.
WC3 was all about the graphics...the FMV and full sound was amazing...and the gameplay (finally a polygon engine!) was much improved. The fighters had distinct personality, and the characters were very real. This would be may favorite game except for one thing...the story was rather trite. They rehashed the whole "Earth is doomed unless we save it" thing, re-gurgitated the whole traitor sideplot that had been thoroughly explored (and better done) in WC2 and Special Operations, stripped out what little content in the game had been put in to make the traitor thing actually make sense, and finished up with you flying down a trench to blow up the enemy's Death Star (excuse me, home planet orbited by big fleet) before they could take out Earth...and your avatar was Mark Hamil. It's like they got afraid of trying anything new with the story.
But WC4--Graphics were the same tried and true engine from WC3, but improved (although I wish they'd left cockpits in). Gameplay was even better...improvements to the AI and deadlier missiles made this probably the most challenging and funnest gameplay Wing Commander this side of Standoff. But where the game really shone was story. The themes it wove were complex and interesting, the villians not black and white like the Kilrathi had been, and some of the dramatic moments were unsurpassed. The moment when Tolwyn orders the Vesuvius around to attack the Intrepid mere seconds from the jump point, and you see the beginnings of panic entering Blair's eyes as he frantically orders a scramble is one of my all-time favorite epic moments in a video game.
WC Prophecy had a thoroughly enjoyable gameplay, and a decent story, but the characters were a little empty (barring Hawk and Zero), and the gameplay was way too easy.
Secret Ops had little soul.
Privateer was too hard when you first started off, and then too easy once you figured out that all you had to do was buy a Centurion and out run everrything on delivery missions.
Never had the chance to play Privateer 2 (though I want to), Academy, or Armada.
If we were to inlcude mods and fan games in the discussion, Standoff would rank just below WC4 in the list of my favorite WC games...