Usually in a game you expect that your toughest challenge will probably be, if not the last boss, at least a boss somewhere near the end of the game. But I've played some games that definitely throw you for a loop on that one and put the hardest (non-secret) boss somewhere else.
The most recent one I've ran into is Alpha Protocol. In Alpha Protocol you fight a boss named Brayko, who you can access pretty early into the game. He's hard to shoot, faster than you, floods the room with thugs which puts you in a crossfire that's hard to get out of, and is a beast in melee combat, which he occasionally tries to force you to engage in by chasing you down with a knife. It took me a lot of tries to beat him, and I thought I was in for a big difficulty spike for the rest of the game. But all of the other bosses were relatively easy, and the last boss was a joke.
So, what games that do this have you run across? Do you think the toughest fight should be at the end, or would you rather have it in an unexpected place for variety?