The best use of transparancy of windows I have ever found is when I run MSN Live at work. I can set the transparancy on any window so I set it to 5% visible for MSN. So when my boss comes in he can not see the MSN window because it is so blended into the background.
Other than that use transparant windows are just a pain to use IMHO. Messes up your head when you can see through windows.
