In thinking about the new atexit module a little more, it occurred to me that I've handled the case where the atexit module gets loaded after another module that wants to set sys.exitfunc (it just incorporates that function into its list of functions), but not if atexit gets loaded before another modules that uses sys.exitfunc. I see two possible choices:
1. Punt and put a bit of verbiage in the atexit section of the library reference manual and the 1.6 release notes.
2. Have atexit.register check each time it's called to see if sys.exitfunc is what it expects. This isn't a perfect solution for a couple reasons. One, there's no guarantee that other sys.exitfunc- modifying code isn't executed after the last call to atexit.register. Two, there's no guarantee that the other code doesn't attempt to be "intelligent" in a fashion similar to atexit (can you say dueling banjos?).
I vote for option number one since there appears to be no guaranteed way to make it work, but I'm open to other suggestions.
Yes, #1 is good enough. I don't think there will be lots of people bitten by this... --Guido van Rossum (home page: http://www.python.org/~guido/)