The worst? Well I don't play MP games so I've not experienced the franchises with really bad reps. But I've spent time on the forums of various SP franchises/genres, and generally found them to be much more pleasant than forums like, well, the escapist forums, for example.
I find it interesting that each game/genre tends to attract a fanbase of a certain type of personality. For example the subsim.com forums (where submarine simulations are discussed) used to be full of people who were highly intelligent, but also very right-wing and militaristic and more than a little bit anal. The BSN, on the other hand, is mostly liberal/left-wing, very gay (in both the new and old meanings of that word) and rather... emotional. The arguments that happen on BSN contrast sharply with the (mostly) cool, rational, and well-researched debates I used to see over at subsim.
TBH I'm having a hard time thinking of a "worst" fanbase because when I do stumble across a bad one I don't stick around for long.