Just stumbled across this article on Smashing Magazine that I thought others on here might find interesting.
The author makes a good argument about what to leave out of your themes option panel including, Google Analytics and favicon switchers. Looking at it from his point of view I have to say I probably agree.
I never thought about the problems that might occur when a user chooses to switch themes if they have let the themes take care of non-theme functionality. Certainly an eye opener.
There are some other interesting points made in the article. Hope it is useful for some