Excellent question. I don't think there's a boxing fan out there that doesn't pine for the days when each weight division had one, easily identifiable champion. Problems arise, basically, due to money. Well, money and politics.
Promoters seem to think that nobody will turn up or tune in for a fight without a world title attached to it, so a whole host of chancers invented their own organisations until we ended up in the ridiculous situation we have now with any number of 'world' titles. Of these, there are four that have any semblance of credibility - WBA, WBO, WBC and IBF.
What you're seeing now is fighters going for the big fights regardless of which body sanctions it because those fights, like Pacquiao-Cotto for instance, are the ones that the public want to see and, consequently, are where the money is.
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There are several alphabet organizations:
WBA, WBC, IBF and WBO are the four most recognized, but there are also the WBF (Evander Holyfield won that title last night beating Botha), IBO, IBC etc etc etc.
Plain and simple, it's all about money!