I haven't heard of any limitations on using custom domains for commercial use, cf. http://groups.google.com/group/google-appengine/browse_threa...
http://code.google.com/appengine/kb/general.html#naked_domai...
http://stackoverflow.com/questions/817809/how-to-use-google-...
http://blog.notdot.net/2009/12/Naked-domains-on-App-Engine
(For non-commercial use this limitation may be more acceptable, but if you are seriously launching a commercial service, you probably want to freely choose your domain.)
I haven't heard of any limitations on using custom domains for commercial use, cf. http://groups.google.com/group/google-appengine/browse_threa...