The Metriod games are good examples of boss fights done right.
The bosses don't have a too many hit points, but you have to find the weakness first. Even then, you can't trade hits because you WILL die if you attempt to. additionally, while the key to beating the boss is usually whatever power up you just got, it is frequently only one of the things you will need. Dodging the attacks is also challenging because the bosses actually have several of them. They are tough, but winnable if you play smart. If you mess up dodging it's not the end of the world, but you can't mess up too many times. Strafing usually dodges an attack, but sometimes it doesn't, so recognizing the attack that is coming is vital to success. Lastly, the bosses usually FEEL like bosses and are usually not out of place. You fight the giant plant monster in the fountain with lots of light and water, you fight the mother ice lizard thing in its home, and you fight the supermutant by the labs where it was created. They give you a sense of achievement while not being too difficult or cheap.
While not all games need a giant monster at the end (L4D has you hold back the horde of regular enemies), it works when thought is put into it and when the game play is until balanced when you know the gimmick/pattern.