In the Wicked fandom, there's Fiyeraba vs. Gelphie. It can get... heated. The Gelphie fandom seems to be the largest, though, probably because of the quite big number of gay people in the musical theatre fandoms.
A common misconception about the Les MisÚrables fandom is that serious Ship-to-Ship Combat exists between shippers of Marius/Cosette and Marius/Eponine. In reality, particularly in modern day, fans tend to leave Marius/Cosette alone and ship Eponine with Enjolras, Combeferre, or Montparnasse, the former of which usually draws the ire of Enjolras/Grantaire fans instead (See the Les Miserables entry under Literature for more details).