Bosses...could go on for a while here:
- First boss (or bosses) of note are a good portion of the cast from Metroid Fusion. The most notable boss here was probably Yakuza (the spider boss,) due to how insanely difficult he was - definitely one of the toughest bosses in the Metroid series. Nightmare comes a close second in terms of difficulty, and any battle involving Ridley tends to be awesome.
- Speaking of Ridley, the two encounters you have with him in Metroid Prime 3 are definitely two of my favourite boss battles of all time. The first battle sees both you and Ridley plummeting down a pipe whilst fighting each other, very similar to how Gandalf fought the Balrog in Lord of the Rings. The second battle you encounter Ridley as Omega Ridley, now more powerful due to Phazon enhancement, which made for a challenging fight with awesome music to boot.
- Giygas from Earthbound, quite possibly the most creepy and downright strange boss to ever appear in gaming history. Upon being released from the Devil's Machine by Porky, he transports everyone to a strange dimension to fight them - Giygas himself is essentially the dimension itself. Between Giygas's strange, warped appearance as a red skull-like shape in the background, the eerie, droning music and Giygas's strange, nonsensical dialogue, this is definitely the most peculiar and freaky boss battle in history.
- SA-X, from Metroid Fusion again. It gets its own, separate paragraph since it was quite unique from the other Fusion bosses in that you actually encountered it several times throughout the game. Most of the time though, you wouldn't be able to hurt the thing, and if it spotted you it would go absolutely berserk and try to kill you...which it could easily accomplish with just a couple of Ice Beam shots. It's satisfying to eventually fight and kill it at the end of the game, although its somewhat poor AI prevented it from being as good as it could have been.
- Sigma from the Mega Man X series. This guy was a pain - he just refused to ever stay dead. You'd defeat him, only for him to revive himself in a new (usually massive) form with which he'd crush you if you'd burned yourself out fighting his previous form. Of course, even if you succeeded in beating him he'd STILL end up surviving and would ultimately end up coming back for the next game. If Giygas is the most peculiar boss of all time, Sigma is definitely the most persistent, and he is certainly no pushover no matter which game in the series you encounter him in.
- Finally, the legendary SOLDIER from Final Fantasy VII, Sephiroth. However, I'm not talking about the battle you have with him in FFVII...I'm talking about the two occasions where you face him in Kingdom Hearts. KH1 Sephiroth was deadly unless you were drastically over-levelled, and even then he could still kill you with ease thanks to his Heartless Angel attack dropping your HP to 1 and your MP to 0 instantly. KH2 Sephiroth wasn't quite as hard to beat as his KH1 predecessor, although he could kill you much quicker than the old one could and spamming Cure spells doesn't work in KH2 thanks to the modified MP system, forcing you to play more carefully against him. Both epic battles, but both unbelivably hard as well.