Dracula in Simon's Quest, for sure.
![Tongue - :p [tongue]](/images/boards/smilies/tongue.gif)
Ok, seriously I'd say Granfaloon. I actually played Aria of Sorrow and Portrait of Ruin before Symphony of the Night, but no matter the game it's always genuinely creepy and disturbing. It's never a huge challenge or anything but it's always a really cool encounter. How often do you see a mass of distorted human bodies floating in the air with a giant laser-shooting monster underneath? Great boss.
I can't remember the name of the "Shadow Beast" in Order of Ecclesia, but I thought that one was pretty cool, too. A neat concept that turned out well. Tough as balls, too.
Portrait of Ruin's final boss encounter with Dracula AND Death together was just beyond epic. There is a fundamental flaw, though. If you just use regular weapons and try your best, you're gonna be dying over and over and over again until you've mastered the patterns. Simply put, it's too hard. But if you went through the Nest of Evil and got the "Greatest Five" attack, the battle is too easy. I would have liked to see a little more balance.
Thinking about it, the series is just chalk-full of incredible boss battles, one after another. The Doppleganger fights are always cool, especially in SotN and Dracula's Curse. And anytime the series pays homage to the first NES game, it's a total joy to play. Namely the marathon, boss rush of Vampire Bat, Medusa, Mummy and Frankenstein's monster before you fight Shaft in Dracula X: Rondo of Blood. (Rev mentioned this one. Good call, bro!!) And Portrait of Ruin does a similar thing for the last remixed/"nightmare" paintings that have one of those four same bosses at the end of each level. The Medusa fight at the end of remixed Circus of Fools is absolutely fantastic.
You know, Castlevania has very very few bad boss battles. I guess that's why it's the best series ever.
Wait, the boss battles in Simon's Quest were terrible (still a great game, though). And remember the giant blob in Harmony of Dissonance? That's the very definition of phoning it in.