I've got 3.
First.
Velius from Final Fantasy Tactics. You can't uberlevel with Tactics because every NPC that you fight is 1-2 levels higher then you. Second, Velius starts off with 3 Ultima demon he-bitches that enjoy summons as much as Velius himself. You were lucky to get a few shots in on him before he wiped you out. Since you don't have Cid, this boss is the hardest in the game, including St. Ajora at the end.
Second and third.
This isn't so much the bosses as it is the games themselves. Gradius V and Ikaruga were so hard I went to sleep with tears rolling down my cheeks. If I wasn't weeping, I was as frustrated as a porn star suffering from impotence.
Getting past the FIRST LEVEL in Ikaruga ranks above figuring out nuclear physics formulas in your head. Gradius wasn't as bad until the third level or so, when you had to destroy a boss that had like 3 forms. (I'm not sure if he had anymore since I kept dying.)