This section seems sadly neglected. Hopefully this reply will spur other people into sharing.
I've had some minor success in rebranding. If you're not an artsy type, I strongly recommend hiring a graphic designer to design the style for you. This means the backgrounds, buttons, layout.
The attached picture shows what a standard user sees. Several of the menu options have been removed or reordered. Tabs have their own individual icons (unfortunately I have not yet found a way to make those icons hyperlinks). Fonts have been altered. Most of the portal icons have been replaced. I made this look almost exactly as the graphic designer dictated.

I'm very interested to see what other people have done. Please share!