When it comes to the big R, Eternal Sunshine gets it mostly because of its language. Yeah, there's a little sexiness between Stan and Mary and Joel and Clem; people have a few drinks; and Rob talks about marijuana. But it's all pretty mild. We should note that if you feel particularly affectionate toward dead birds, one of Joel's memories might be a bit disturbing. And speaking of disturbing, some people don't really have faces; there's just sort of… skin where their facial features should be. It's creepy.
But other than that, the main thing is that these characters pretty routinely drop F-bombs and other expletives. There are a lot of mad, sad, and generally upset people in this movie, so it's really no surprise.