Whatever his name is from Crystalis: I played this for the GB. I found this thing called the wizard ring which gave me beams from my sword regardless of health, and the final was a matter of simply repeatedly pressing B from farther away than he could do much effective.
Xenosaga II: They just fucked this up so bad. (The entire game, but the final boss was a special fuck up). The "real" final boss had no dramatic music, no final form, no exotic dancing girls, etc. So when you thought you reached the final boss, even with time in between to save, it was a storyline battle. Storyline battles require proper timing or anticipation: For example, FFVII yay, FFX boo. XSII OMGWTF.
Xenosaga III: Meh, by the end of the game I had strategy figured out pretty easily, so there wasn't really any effort required for the bosses in the final dungeon. There was this item called "Seven Moons," available at normal shops in the early part of the game, that revived + fully restored HP/EP. So the best method of healing was to let your characters die one at a time, which wasn't hard to do.