The main repo which come with the install, plus volatile and security (also with install).
The ones who need might add "contrib" and "non-free".
Assuming one runs stable one could use backports.
http://backports.debian.org/
The other repo which is used often is the multimedia repo. That is not official, but used by a lot of users.
http://www.debian-multimedia.org/
Not that sure, as i don't use flash anymore, but in the past there was a slightly difference between flashplugin from the debian-contrib repo and the the flashplugin from the multimedia-repo.
All other repos are official Debian repos, and hence fully compatible.
To give an example: as far i can tell the aptosid forum does recommend to _not_ use the multimedia repo. I don't think i had big problems with it. Anyway: though often used, it is _not_ official.
bout pulseaudio i don't know. I ain't got it installed