WC2 is a stong contender for me...certainly the most emotionally powerful. However, it misses out because I wasn't at all crazy about its gameplay--in fact, I liked its gameplay the least out of any of the WC games that I've played except for Privateer. (I've played WC1, SM1+2, WC2, SO1+2, WC3, WC4, Prophecy, and about half of Privateer, Secret Ops, and Standoff).
My favorite has got to be WC4, though. Unquestionably. For the following reasons:
*The AI is awesome. Seriously, WC4 had the best AI of any flight or space sim I've ever played. In every other game (WC and otherwise) the AI seemed to consist of a bunch of preporgrammed maneuvers that you could learn to anticipate--i.e. it always felt like I was flying against a computer. In WC4, for some reason, it almost seemed I was flying against a human. It did weird things I didn't expect, like a Vindicator skimming the ground and then diving for the deck, getting my faster Hellcat to overshoot, and then popping up behind me and nailing me with a HS. The enemies worked effectively in teams, and made being outnumbered really suck, just like it does in real life. The thing about Prophecy that disappointed me most was that the AI seemed to take a step back (then I figured that that was just because they were a bunch of bugs and not people.
*Great story. Almost as good at WC2 for emotional content.
*Fantastic acting. The greatest moment in any video game I've ever seen (spoiler ahead) is the moment in WC4 where the Intrepid is chasing the Vesuvius, and Tolwyn calmly orders her to turn around and attack, commenting about kicking a junkyard dog in the teeth, when the camera cuts to Blair's widening and suddenly panic stricken eyes as he orders all hands to battle stations. Great climactic moment!
*I know other games have done it since, and probably some did it before, but I loved the WC4 had different endings and made judgements about what kind of person you were based on the choices you made, some seemingly insignificant. I got the "evil" winning ending my first time, and was quite upset about what that said about me!
*Very good gameplay. Nice graphics, missiles for once were actually useful, I liked the controls, I like the capship interaction.
All around, probably one of the top five games I've ever played, of any genre.