Command and Conquer Tiberium Dawn (and pretty much all of the Tiberium series): Hands down the Brotherhood. Playing GDI it just felt like the standard "good guys" vibe. But with NOD...You felt a part of something bigger. It did help that Joseph Kucan just oozes malevolent charisma when playing Kane.
Its long past the point of spoilers, but the moment where Kane shoots Seth and says simply, "I am Kane" still sends shivers down my spine.
RA 1 (And expnsion packs): Russia. Missile subs, heavy and mammoth tanks, yaks, migs... in terms of raw unit firepower Russia takes the cake.
RA 2: Brits. Be green, hide snipers behind trees, anytime there's an infantry push hillarity ensues. Either that or France and just daisy chain power plants until you make the Great Wall of Grand Cannons.
RA 3: Japan. On any map with water Battlecruisers dominate the long range game.
Generals: GLA! So adaptable, and the lack of having to manage power is always a huge plus.
CoH: Panzer Elite in Company of Heroes hands down. Some of the hardest hitting infantry, adaptable, fast moving. Fits agressive playstyle perfectly.
DoW: The Necrons were imba. Crazy imba. Without the forced retreat rules from tabletop, it gets REALLY hard to stop necrons.
DoW2: It's a tossup for me between Chaos (Blood for the Blood God!) and Orks. Chaos is fun to play, Orks are even more fun to listen to.
Homeworld: Kushan, drone frigates, cloak fighters. So many ways to harass resource lines more than the brunt force of Taiidan's
Homeworld 2: Vaygr. I know theres not much difference between the two factions, but I like the style of their capital ships and fighters more.
Sacrifice: Have to say, playing for a giant celestial Earth Worm Jim has its appeal.
KABUTO: KABUTO WILL EAT YOU.