For the ultimate campaign villain, yes, like many other posters I go human. It's from a desire to not add editorial comments about race/social class/whatever into the game and also to deny the characters the ability to look up stats in a monster book. I've always felt that the biggest fights in drama are between individuals, not races or cultures, and highlighting nonhumans in this vein reduces the choice to fight into simplistic terms of "us against them." In such cases, fighting nonhumans usually makes the choice to fight too easy for my tastes...
Academic analysis aside, I do favor certain critters for my games, just like everyone else. For brutal, savage humanoids, I use gnolls. I just got tired of the idea that orcs are somehow like klingons in their culture. I still use orcs in my Greyhawk games but not my homebrew. I'm considering reintroducing them as a race that used to reside in the abyss and were expelled to the material plane. This would give them easy, obvious ties to the various demon princes and other established bad guys in my ongoing campaigns.
For clear-cut bad guys, I usually use undead. Their abilities and immunities usually make them relatively tough for their CR (especially if the party lacks a cleric or paladin). For 'dangerous simply because they're dangerous' encounters, I favor constructs, animals, and elementals. I use a pretty hefty amount of demons and devils, who are intelligent and organized enough to make a credible long-term threat and also instill a sense of fear in both the characters and their players.