yeah the xenogears final boss really gave me a hard time...especially after getting all my fuel sucked out of me...i barely made it out alive...i think that silly looking pink thing saved me big time...
hm...what else...Dracula at the end of Circle of the Moon was rough too...especially since i went in pretty low level and without 2 cards that eventually allowed me to beat him...
the most frustrating would have to be the big brain thing (nil-something) at the end of half-life who kept zapping you to other places and you had to jump into these teleportation portals to get back (only they were situation on the ceiling or somewhere less than cooperative)
oh yeah...near the end of max payne was really rough too...you had to be a quick-save whore to get past anything --- turn the corner, quicksave, dive out and shoot in bullet-time, quicksave, damn i missed, quickload, shoot again, missed, quickload, shoot again, a hit, quicksave...