Your/you're is a biggie. There/their/they're is another one. Hear and here. Too and to. The simple ones, that most people just... I don't know, it doesn't take some great intellect to do it, it should just come naturally, if you read at all and English is your first language. But man, when I see someone writing some big thing, and they are messing up homophones... well, there is usually a direct correlation between that and the quality of the overall post.
People also struggle with apostrophes, but that one... I don't know, it is a little more understandable I think.