Personally I think it's the goddamn panel; I've never seen a Linux panel that looks as nice as its counterparts on Windows and OS X. It seems like a small component, but it really "frames" the whole desktop environment -- like a drumbeat -- and in both OS X and Windows there are some complicated gradients in the panel that I'm almost certain were insisted on by some tweed-clad hipster with a title half a sentence long; to my eye it really does make a difference.
The windows actually look really nice, especially considering it's the default skin.
It takes a professional designer (or rather, a dozen of them) to produce a professional-looking desktop theme. Which is exactly what the majority of FOSS projects lack.
When you let a programmer dictate the design, you end up with a lot of features and a lot of misaligned margins. In my experience, many programmers just don't care about pixel-perfect designs. Yes, I'm talking about the same group of people who scoff at typography because "the content is the only thing that matters", blah blah blah. Admittedly, I have no data to back this up, but I have a gut feeling that lightweight desktop environments are particularly teeming with this "function before form" crowd. When you treat design as a second-class citizen of your project, it's no wonder you can't attract good designers to work with you.
On the other hand, when you let a designer dictate the design, you end up with perfectly aligned margins and anti-aliased corners, but all the features and configuration options you care about are hidden behind five clicks and a keyboard shortcut, or worse, removed entirely because they somehow violate the designer's philosophy :(
The windows actually look really nice, especially considering it's the default skin.