I dont know about the complete hisory of boxing, but I enjoyed the Barrera/Morales rivalry. These guys dont like each other for real, which always made it interesting.
Ali versus Ken Norton comes to mind. Especially since Norton was jobbed out of the title. Ali had the look of a fighter who knows he has lost when the decision for him was announced. Norton cried. Truly a bad decision.
Ali / Frazier - as good as it gets Gatti / Ward - some what of an arcade rivalry, but still, those fights were amazing Marquez vs Vazquez - two as equal fighters as can be.. both can box, slug, punch and neither chose to defend. Holyfield vs Bowe - big guys slugging it out bigtime Robinson vs LaMotta - the fights that cemented Robinson and gave LaMotta his name - all great fights. Benn vs Eubank - the greatest rivalry on british soil
You can still add a poll after your thread is set up. You just edit your first post, go to advanced options and i think (from memory) thread tools. You can change your title among other things as well!! Otherwise, i would say Ali/Frazier for sure, simply because of the magnitude of the fights, and their position in the sport.
I guess Morales v Barrera is a good one also, and if you wanted to start going back a bit further, Robinson v Lamotta and Pep v Saddler really stand out IMO.