I would certainly have to chime in agreement on the Metroid Prime bosses. Meta-Ridley and the Omega Pirate both make for smashingly good battles, especially the first time you encounter them. The last time I'd played that game, I went through it on Hard Mode (since I'd beaten it a long while ago) and was completely blown away by those later boss fights.
Some turn-based RPGs have actually blown my mind with bosses before, of course not due to twitch factors but mostly due to the overall atmosphere of the fight (i.e. music, etc..) . The first that comes to mind is the Yunalesca battle (and various intermediate Seymour battles) towards the back half of Final Fantasy X. For me, those battles ended up being more decisive and memorable than the ones that followed at the very end of the game. I would guess it's because of the 'Challenge' theme that blind-sides the player with a very aggressive effects-laden sound palette, a piece of music that is essentially all about ramping up tension...no nice Uematsu melody to soothe you along or give you hope.
Others that come to mind are several of the battles in Skies of Arcadia Legends. I always liked the way the music in those boss battles would change according to how the battle was going, at turns becoming either excruciatingly tense and panicky or uplifting and triumphant. As such, the more tricky battles like the optional bounty hunts probably made for the most nerve-rending and exciting fights.
Finally, I'm about 15 hours into playing Grandia II for the first time and have really enjoyed the few major boss battles that have occurred. The battle with Valmar's Eye was a particularly chaotic delight, as you're forced to wrangle a small swarm of those annoying eyeball bats that fly every which where, all the while having to remember that the boss is also there to whip your ass with brutal status assaults, etc.. The battles may not be that hard, but the atmosphere of them is delightfully frantic and exciting. As well, the nature of the fight puts a lot of weight on your turn-based decision-making. While an action-RPG like Tales of Symphonia may look the same on a superficial level, I always thought that the A.I. spamming and fighting-game mechanics made the boss fights in that game pale in comparison.