Then there are "Setting Wars", for example Vampire vs Changeling for WW, or Greyhawk vs Forgotten Realms for D&D. And lord help you for D&D if you like Spelljammer, Ravenloft, or some other minor setting.
For Forgotten Realms, The Wall of the Faithless in 3.5e is a sore point among many gamers.
In many communities, discussing game mechanics or strategy at all has been known to incite shrill rage from players who feel the focus of these games should be on "roleplaying" to the total exclusion of mechanics.
"Traditional" role-play games (generally speaking the ones with a Dungeon Master) vs. the new "Narrativist" movement. Don't dare to say that "Everybody should choose the way of playing he likes the most". You have been warned.
In the Warhammer 40,000 fandom, this may apply to the two missing Primarchs or to whether or not the Emperor is really all that great. Most of the newer Codexes (particularly the Blood Angels, Grey Knights, Space Marines) and anything about Matt Ward have been causing a lot of cries of "HERESY!" Necrons, surprisingly enough, less so. May the God-Emperor help you if you ever mention female Space Marines.
Character Alignment. Applies to alignment of given characters, what alignment system to use, and how to use it.
An experiment you can do at home, but probably shouldn't: start discussing morality or Lunars on an Exalted forum. Odds are good within thirty posts everything will be on fire. Thirty posts after that someone will come and burn your house down.
Specific mention on Exalted morality: RAPE! Should canon books features rape, both fluff-wise and as super power? This is largely the reason why some people hates Infernal splat, usually loudly so. The omnipresent trope in Exalted is exercise of power be it fair or foul, and it would be an injustice to not include rape, including supernaturally empowered acts of rape.
There have been many remake of D&D 1st edition, leading to a resurgence of Old School play. Topics such as "Old School vs. New School", "Rules, not rulings", "System does/doesn't matter" can be beserk buttons for certain people.
Netlisting- Are people who do it just using whats been proven to work without having to reinvent the wheel, or "Stop Having Fun" Guys who are using someone else's hard work to get ahead without trying. Also, how much do you have to deviate from a tournament winning list to for it to not qualify as netlist?
Attempts to examine the moral implications of violence, alignment, and/or monster "races" in traditional fantasy Role-Playing Games, particularly D&D, descend into flaming chaos and Godwin's Law within about three days.
For reasons that will forever remain a mystery to all who did not witness the written carnage for themselves, the D&D forums on the Wizards of the Coast site had to put a complete moratorium on the subject of the katana and how it compared to other makes of sword in the ancient world. There's really no adequate way to explain this, but suffice to say circumstances really did force their hand.