I think the big thing is that most open source software is done on Linux, while most proprietary software is done for Windows and Mac. On Windows and Mac you have only one, native look and feel, to which all apps try to conform. On Linux, every distro looks different, and a big part of users doesn't want GUIs at all, so they consider aspects like look and design secondary. On Mac and Windows most users want GUIs for everything, so it's more important to make those GUIs look and feel good.
Windows doesn't really have a uniform look and feel. It has a sort of ideal at any one time, often led by whatever Microsoft are doing with the next version of Office, but the result is a giant mishmash of things written at different times using completely different toolkits and themes.
I think the big difference is actually that commercial software entities can hire UX people to design their user interactions. Open source projects generally have nobody with that kind of skillset, and if there is any money available it gets spent on core programming because there are masses of bugs to fix and features to implement.
