I have run into some show-stoppers in PHP 5.3 stable, including PRE-INIT queries with mysqli for which a bug was reported and patched in 5.3.2 DEV, which I had to pull from the snaps to get a domain running properly on a development site. IMHO, I would let 5.3 mature a bit more before using it for a live implementation. Use that migration guide for sure. There are other areas that may impact you.
I have a PHP 6 install too but haven't had as much time to dedicate to testing on it. I was actually a little surprised when they first announced the 5.3 branch but there must have been something in developer discussion that prompted the interim release.