Metal Gear Rex from the first Metal Gear Solid game is one of the most intense boss fights I've played in a game. I like games that are able to actually have a realistic large scale enemy, and Rex is probably the most convincing one I've seen in a game. Usually, large things in games just have the "Final Fantasy" effect: it doesn't matter how big it is, in reality it moves exactly the same and is just as powerful as something much smaller. Rex managed to actually seem plausible despite it's ridiculous size, and the entire fight seemed like an actual David vs. Goliath battle of epic proportions. Plus you actually had to use a bit of strategy: hiding behind boxes out of it's sensor sweeps, using grenades to scramble it's electronics, dodging the heck out of the way when it makes a mad charge at you like a 100-ton bull.
Here's a picture of Rex for the 5 of you that haven't played the game (the Twin Snakes version, but eh, same thing):
http://www.home.no/lzp/Rex.jpg
The Azel/Atolm battles in Panzer Dragoon Saga were also a treat, in fact many of the boss fights in that game were spectacular for an RPG. Rarely could you ever win simply by hitting attack over and over again. The only problem was that the game was fairly easy, and some parts of the combat system were pretty broken (like the counterattack spell and Sniper gun attachment).
Jam it back in, in the dark.
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