UT2004 certainly does have a much more forgettable look. But the look and style of Quake always seemed kinda like a step down from Doom to me, I guess it's the little color and enemy models. However, you can definitely instantly recognize it's Quake from any screenshot, that says something too.

But keep in mind the question was "favourite" ugly game, I didn't mean to say anything bad about Quake. It's ugly in the same way that some awesome metal genres sound ugly.