This is funny to me, because until my 1st 2k8 installation Christmas week, I didn't know that SQL Server would actually append to an existing disk file. That didn't stop me from anally not selecting 'Append to existing media" when doing a manual backup.
Size, simplicity, manual file manipulation. Those are all good enough reasons for me. I wouldn't want to be the stranger picking up the pieces that came across something named "ALL_SYSTEM_DBS.BAK." There really isn't any difference between multiple DBs in a single file, and multiple files in a single folder.
I'll stick to separate files.