Dark Crusade for me considering I've only played Winter assault, the original, DoW II, and that's pretty much it :/
I've been playing the Dawn of War series since 2005 and without doubt my favourite was Dark Crusade, second would be DoWII Retribution mostly because of General Castor moustache and ability to shoot one handed a sniper rifle.
Dark crusade and Retribution, Dark crusade was kinda sorta balanced which was kewl, and retribution has horrendously English imperial guard, that pleases me
After extensively playing all of the games listed here extensively, I gotta go with DC. I loved the dialog between the commanders, and who does not like seeing necrons own everything aside from those loyal to the Emperor. I loved the story line for all of the games, ALL of them. Also, Dark Crusade was the first 40k game I have ever played. I still remember my first thoughts as I was puzzled why two forces fought each other when they clearly fought for the same Emperor. Or what made space marine weapons so different from modern weapons. Or that for a while I never realized that the tau were aliens. Yeah, looking back now it makes me simply feel silly.
I loved the Dow2 story, but I voted Dow2 Ret because it was so much more expansive. I didn't play chaos rising though, I have a feeling that would have been hands down the best.
The Last Stand mode on Retribution as also a huge amount of fun. Long nights just trying to beat that final wave...