Read the GNOME Human Interface Guidelines. These are pretty good guidelines developed by some interaction design professionals, and are the best guidelines to come from the open source community so far. Until we have official Fedora Project guidelines, following the GNOME guidelines will probably result in a substantially better UI than making up your own. And our tools will be consistent with each other and at least one desktop environment.

Of course you — and everyone else — will disagree with some of the guidelines. That's fine, but recognize that if everyone violates the guidelines in the 10 places where they would have done them differently, there's no value to having guidelines. Avoid silent civil disobedience, but feel free to file a bug report.

The GNOME guidelines will only apply to X11 applications, obviously, not to web applications.

Remember that UI guidelines are mostly about details - laying out your widgets properly, and such. Don't get too bogged down in this and neglect the big picture. You can be fully guideline-compliant and still have an application that doesn't make any sense.