I have mail accounts through google apps on a few different domains and it drives me crazy that I cannot customize the theme as I can with gmail. So a simple workaround: use a free gmail account in tandem with any google apps account that you use enough to desire a theme.
Within a free gmail account, it is easy to send all mail through a different account; in this case, send mail from the google apps account. Then on the flip side, forward all mail into the google apps domain into the mailbox of the gmail account. Voila! Use the gmail account with all the power you're used to, and nobody will know....unless they see that logo has changed ;)