The culprit of Umineko: When They Cry. Shkanon theory that claims Shannon, Kanon and Beatrice are the same person vs. Rosatrice theory which puts Rosa and George as the main culprits on the gameboard. The arguments can be fierce, both sides declaring the other theory nonsensical, with red truths flying all over the place to "prove" it. By now the Rosatrice theory has been completely jossed, but that hasn't stopped arguments from popping up every now and then.
Arguments over the original and PS2 port art rages, with many who either think the PS2 art is superior because it's drawn professionally, or those who feel the PS2 art is too generic and loses much of it's charm.
There are arguments over sub-genres of Visual Novel - especially between Nukige (Excuse Plot Porn), and Story-driven games like Steins;Gate and CLANNAD - the latter think the former gives the genre a bad reputation, while the former think that the latter are snobs and prudes.