Has anyone fought the Boost Guardian from Metroid Prime 2: Echoes on Hard on the original GameCube version? That guy was NOT easy (even on Normal mode). I throw in some of my favorite bosses from games that I've played...
Seven Force (Gunstar Heroes and Alien Soldier/Genesis)
For obvious reasons...
Abyssian (Tales of Symphonia/GameCube)
This guy is just insane (especially on Mania mode). He has all sorts of demonic weapons at his disposal and his attacks hurts like hell. He uses a lot of your characters' techniques and spells like Tiger Blade and Eruption. But that's just the start: in the Japanese-only PS2 version of the game, he can also use Shining Bird, Divine Judgment, Indignation Judgment, and Lloyd's Falcon Crest.
The "True" EVE (Parasite Eve/PS1)
[spoiler=Parasite Eve]You are fighting Aya's biological sister who is the original mitochondrial Eve. She has some really annoying attacks that inflicts status abnormalities like slow or numb and she has well over 42,000 HP, which is a lot in this game. She also had this attack (if I can recall recorrectly) that was like Sephiroth's Heartless Angel and can reduce your HP to 1 in and instant. Plus she can use her version of Liberate against you, which can hurt like hell if your Defense and HP is weak (though I fought her with an armor that customized to have a fair amount of Defense and the highest HP enchancing ability at Lv. 99 that give me 999 HP).[/spoiler]
Sephiroth (Kingdom Hearts 1/PS2)
What this list my favorite bosses be with him in the line-up. But seriously, at lower levels he was the hardest boss in the game. I have a very vague memory about fighting him the original Kingdom Hearts since I haven't played in over 5-7 years. But again, fighting him was worth the EXP.
Gary/Blue (Pokemon R/B)
This guy because he can assemble a team of strong Pokemon with a wide type coverage and he had the most epic boss theme from the 1st Gen games.
Red (Pokemon G/S)
A huge step-up from Gary with a team of Lv. 70-80+ Pokemon.
Iris Zeppelin (Rosenkreuzstilette ~Blades of the Rose Cross~/PC)
[spoiler=Rosenkreuzstilette story and plot]This is a boss I was not expecting. She kills her own father, falsely imprisons a man who caught onto her plans (Karl Palesch, Liebea's brother), and uses a military unit to start a war with an empire while watching the game's heroine fight against her own friends. All for what: to alleviate her boredom. Iris is the type of boss who makes me say "How dare you do that!!" because she is bored of everything in the world and she decides to toy with people with her god-like powers and intelligence to devise such a plot. And she is certainly no pushover, either (namely in Rosenkreuzstilette ~Grollschwert~), being a hybrid of the Wily Capsule 5 from Mega Man 5 and Lumine from Mega Man X8 after all.[/spoiler]