When it comes to boss fights, first of all I think too many games get stuck on the "default" idea of a boss being a really big enemy with a lot of health. That format isn't conducive to every genre or franchise. If you have bosses in your game, you need to tailor them to the game's mechanics. A proper boss is supposed to be an advanced test of the player's grasp of the mechanics.
Most games don't even really need bosses, but have found few or no other ways to have climatic events. Why couldn't Prince of Persia games just end with a really tough puzzle or platforming section? Why couldn't Assassin's Creed just end with a place that's really hard to sneak into?
Half-Life 2 did a pretty good job approximating "boss" battles to its own mechanics. The game's only real "boss" is a helicopter that hounds you for an entire level. You also have the climactic fight in nova prospekt which many agree is the hardest part of the whole game (I still can't beat it without using exploits). In my opinion HL2's real climax was the battle at the horse in City 17. The episodes also do a good job with battles that still feel climactic without being conventional "bosses".
But the one modern game I think did the best job of twisting conventional boss battles to its own mechanics was Metal Gear Solid 3, which used them to illustrate its mechanical themes.
The End is currently one of the most popular bosses ever because in order to beat him you had to actually use the stealth skills you learned up to that point in the game. One thing to note is that this boss occurs pretty much exactly halfway through the game. It's also the last jungle area you encounter before moving on to the mountains and the more urban-style secret base. That fight is sort of like a final exam for jungle stealth. And then they bring some of that back for the final battle against The Boss, which also required mastery of the skills you use the most in Metal Gear.