Trypticon from WfC: just cause it's a battle on an epic scale (Omega Supreme's battle sucked)
Snake VS Liquid Osalot and Rex VS Ray in MGS 4: i like the 'mood' surrounding the last boss, and Rex Vs Ray, ripping shit up in giant robots, fuck yeah
Blood Lord, Titan and Elchulus, Vindictus:
Blood Lord was the first raid boss in the game to actually be a challenge, he teleports, has an attack that dose 2K damage (which is a one hit kill if your fighting him at an even level) and is just fun to fight
Titan was the first raid boss to have an unblockable attack, which sounds like a 'dick move' but in practice, it was executed very well here, its gotta long wind up so you get tagged its your fault really.
Elchulus: big ass red dragon that flys, breaths fire, can almost take an hour to kill .... and you need more then 8 people (standard raid party size) to take him down, you need around 20-24, again, first boss to 'need' that many people to bring down (if you hadn't picked up on that patern yet)