Privateer. Hands down. I have played more hours of Privateer on its own than I have nearly every other game I have played put together. Well, maybe not quite that much, but darn near it. The main game is pretty much the perfect open-world space trading sandbox game, and manages to do so with a pretty awesome main story, to boot. They manage to real you into the main storyline by giving you some... unique rewards... for completing them. Basically, this game takes all of the stuff that was awesome about Elite and Frontier, but strips out a lot of the tedium and makes it more fun and engaging. Sadly, the only feature present in Elite that is missing from Privateer is the ability to mine asteroids. You can sink many, many hours just trading goods back and forth across the 70 or so planets spread across Gemini sector, taking bounty missions, becoming a pirate, mercenary, or a vengeful destroyer of Retros. HOWEVER! That's only half the package!
You ALSO get the Righteous Fire add-on, which adds a whole new story line to go through, with its own selection of unique missions, as well as new equipment for your ship. You can still continue to just ply wares or sandbox in any other way to your heart's content, but RF is a fun and action-oriented plot that is rewarding in itself to play through.
I'll admit that I haven't played much of Privateer 2: The Darkening, which looks like a pretty decent game, but doesn't seem to have quite the depth of Privateer.
As for the rest of the games in the series, it really depends on what you are looking for. I have a very special place in my heart for the first three games, especially WCII.
WCI isn't quite as stellar as the rest, and the story is just kinda there to give you a reason to fly around blowing up space cats, but it more or less defined the genre in its time.
WCII picks up where WCI left of, pushing the spacefighter sim state-of-the-art in gameplay, but really breaking through in its more well-realized cinematic presentation. The story was, for its time, one of the most involved and well-written stories for a non-RPG.
WCIII again upped the ante on all fronts, presenting us with live-action cinematics driving a narrative that made each well-crafted mission that much more meaningful to fly. I also think this is the first game in the series where you are able to specify your craft's weapons loadout, and even change which fighter you are using on a mission. After about the first ten minutes, you really begin to think of Mark Hamill as Christopher Blair, and not Luke Skywalker. Unfortunately, it is still a literal impossibility to think of Malcom Mcdowell as anyone other than either Emperor Caligula or Alex DeLarge.
WCIV yet again upped the ante in cinematics, told quite possibly one of the more convoluted stories yet seen in a game that wasn't either an RPG or a point'n'click Sierra/LucasArts game, and delivered more refined (and difficult) combat.
WC:Prophecy (never TECHNICALLY titled WCV) was to be the beginning of a new story arc, featuring a new main character, and pulled back on the cinematics in an effort to offer a tighter gaming experience. The flight engine was top of the line when it released, and still holds up pretty well by today's standards. A lot of people dislike the game more or less for no other reason than because Blair was not the protagonist. While I loved the cinematics in WCIII/IV, mostly for proving that video and computer games could offer more than just "clicky clicky, boom boom" and were capable of delivering epic narratives in a truly compelling way, I kind of enjoyed Prophecy's departure from that spectacle. It still has excellent cinematics, mind you. They're just a lot more conservatively used.
The oddball titles are WC:Academy and WC:Armada. Academy is basically just a mission editor flight simulator. It's the simulator cabinet from WCI and II with the ability to make almost any type of mission you desire. It's fun for some quick WCII-engine dogfighting, but there's really no story, or any real reason to play it beyond seeing just what kind of insane missions you can devise (and survive), and seeing how long you can survive the pre-packed "Gauntlet" mission.
Armada was a fun little title, in its day. I used to play this game quite a bit over direct modem connection with friends. It's a simplistic strategy game where you play either versus the computer, or versus a friend over network or modem, and you each take turns capturing planets to collect resources needed to build fighters. You can skirmish with each other over control of the planets, with the ultimate goal of destroying your opponent's capitol ship. The real fun to be had is the rare ability to fly a variety of Kilrathin fighters. Armada was a novel concept, and still holds up about as well as WCII, considering it uses the WCII flight engine.
Out of the entire series, the only one that's really an easy pass is Academy. Every single game in this series is worth playing, from beginning to end, at least once. Especially for fans of spacefighter sims. If you have enjoyed space combat games, or enjoy the kind of cinematic experiences we now find in Mass Effect, Halo, or even Call of Duty, you owe thanks to Origin and Wing Commander for providing the test bed. Tip your hat, son! Or daughter, really. Sexism is so passe!