A holy war is a dispute, often but not always over a relatively minor issue, which is not resolvable on the merits of the arguments, but where people feel passionate enough to continue arguing anyway in the hope that their side will prevail. Holy wars are not quite the same as bikeshed paintings. People painting bikesheds are usually quick to jump in with an opinion (because they can), but they won’t necessarily feel strongly about it, and indeed will sometimes express other, incompatible opinions, to show that they understand all sides of the issue. In a holy war, on the other hand, understanding the other sides is a sign of weakness. In a holy war, everyone knows there is One Right Answer; they just don’t agree on what it is.
— Karl Fogel, Producing Open Source Software
I think, too, that bikesheds are more obviously trivial – the participants might have rational that matters to them, but an outsider can quickly realise see that the outcome doesn’t really matter all that much. Whereas a holy war is more complex – both sides have valid arguments, and fully understanding those arguments is almost impossible. They also tend to be a lot more factionalised, and ugly.