Hmmm.... difficult to choose one or me, not because I don't think there have been any good bosses, and nor because there are so many standout candidates either. I just have trouble thinking of an answer; ask me 20 times and I'd probably give at least 5 different answers.
For me, it is probably more a question of what the best boss fight is rather than the best boss outright. The Alastor fight from Painkiller was really memorable, the way he stomps and literally makes the level fall apart around you.
A classic choice would have to be the Cyberdemon from Doom, for all the right reasons. Big, strong and carries a massive rocket launcher (and a proper rocket launcher from the Doom days at that - even if you somehow survived would leave your screen red and fling you up against a wall, not these pansy peashooters you get nowadays). Stays true to my preferred boss design i.e. no gimmicks required to kill it, just a ton of firepower.
Slightly off the wall choice but Shivan Juggernaut from Freespace 2, when you distill it down to the base properties, has plenty of characteristics of a good boss i.e it is completing ****ing badass while retaining an air of mystery, and instilling fear in the player - one wrong move and that beam cannon could seriously ruin your day.
You know, I actually think bosses are one area where some mediocre games can compete, by which I mean that we always tend to think about bosses from the best, most enjoyable games, but there have been some pretty good bosses in otherwise unremarkable games. I was playing Infernal earlier this year, nothing special as a game, but the final boss section was pretty good I thought. Tribes Vengeance had some good bosses too as I recall.
. Shame they ruined him with the 'new' Nemesis, sounds like a bloody pirate, yarrrrr starrrsss! 
