I liked Wesker in RE5. Not the boss fight in the volcano, but the one on the tanker. There were just so many ways in which you could trick and hurt him. Me and my friend had a blast trying to find them all. Perhaps if Wesker didn't always wear sunglasses, turning the lights off wouldn't have made him blind.
With Birkin you had to switch tactics halfway through because he would transform and the fight could get really hairy if you didn't save any magnum rounds for his 2nd form. Not to mention the timer really added a sense of dread.
Mr.X was the Nemesis of RE2, stalking you everywhere then finally transforming into a Tyrant after you throw him into a pool of lava and holding out until Ada throws you the Rocket Launcher.
Faceoff with Wesker & Jill in RE 5. I just really liked how he seems essentially invincible unti you get smart and start using hit & run strategies.
Also, Krauser in RE 4
Those tend to be my favorite kinds of boss fights in games on the whole. The threat really seems dangerous and has a lot of advantages over you, but you can win by finesing them or thinking your way out. Some of these mega bosses in games just seem bloated & helpless by comparison.
Black tiger - the giant spider in resident evil 1 Nemesis when he's at the clocktower and he's all tentacly
I cant decide between Yawn the giant snake from RE1 or the giant invisible snake from RE6 for the 3rd one.
I dont like most of the boss battles in the recent RE games , the developers treat you like you completely retarded and put big bright orange and red pimples on the enemies to show you where to shoot. Its more fun finding the weak spot on your own!