This is by far the most requested feature (in my opinion) by the users of Windows Mobile devices that I meet wherever I go. "How can I change the UI? How can I replace the Today screen? How can I have my own program launcher?".
Rabi Satter, one of our consultants in the Mobility SST (SWAT) team posted recently about how today, with Windows Mobile 5, you can create your custom shell, although it's more of a hack than anything else.
I can't wait to see more custom shell and skins for Windows Mobile like the JGUI's Vista skin. I know, we don't have support for developers to build that into our shell easily but don't worry, we're working on it. :)