Most of my difficult fights have already been mentioned, so I'll quickly comment.
-Justice (Guilty Gear) is very tough, yes. It is possible to Destroy her, but it's very difficult. If you destroy anyone through the main game, you increase the chances that Justice will Destroy you. ugh.. However, I got very good at juggling her with Axl. Baiken's not bad, she's just defensive.
-Hitoshura (SMT DDS1) Never managed to clear this fight before I had to return the game to a friend. Totally agree that this boss is made from pure liquid "FUCK YOU". I have no idea what the Red Star strategy is, though.
-
(FFXIII) All fights are difficult, yes. I had the most trouble with the very first fight in Chapter 10, due to mismanagement of equipment. My problem with these fights is
*sigh* .. and yes many of the optional fights in the game fill me with rage.
My contributions: (those that quickly come to mind)
-Stage Bosses 5 & 6. (Blaster Master)
Boss 6 can easily be taken down if you use a glitch that attacks him while the game is paused. Otherwise, you'll have a very hard time hitting and dodging his claws, as they are very quick and very long. Boss 5 cannot be killed by the aforementioned glitch, so you have to get right up close to him to attack. This one spits out more and more bubbles as the fight goes on. They're in a bit of a pattern, but he moves while shooting, so that throws things off.
-Elecman (Megaman)
With the Rolling Cutter, this boss is a cinch. But why use that? Go ahead and fight him without special weapons in a game without sliding, Mega Buster, or Energy Tanks. It definitely doesn't help that Elecman is very quick, and can kill you in 2-3 hits. He is the only boss out of all of the games that I couldn't defeat with the default weapon.
I'm sure I'll remember more later.