The boss that gave me the most trouble that I can remember was Miguel from Chrono Cross. Square did a great job making a bitch of a boss look like a complete pushover.
I second this, he was a prick with his glowy lightsaber., and MAIN CHARACTER being a dark element at the time. Goddamnit SE put out a PSP port of chrono cross already!
I third this. it was very hard to keep your entire party alive due to Whitesword and the face your main had a weakness to white elements. Don't even try to bring any characters who innate element is black due to that skill itself.
Though for that boss fight it introduce some needed stragegy against him. Though the later Lynx fight was pretty nasty as well, But the....
Dario fight tops them all considering it is the hardest fight in the game which gives you a very strong weapon that makes the later bosses a lot more tolerable.