I have to say, that I think the worst Boss of all time has to be Dr. Willard in Tomb Raider III. Not only is it rather intimidating to have to face a giant, otherworldly, spider-thing--but he's invincible, too! You have to run all over the damn place picking things up while avoiding his instantly-fatal acid spray and not getting trampled. Not to mention the pools of acid surrounding his happy little bubble. Damn bug.