You should be able to run something from crontab overnight to restore the correct (non-nobody) ownership to those files and then reset quotas. Just an idea.
Of course the real fix is to run phpsuexec and suexec. There are a heap of other reasons why that's a good idea, including that it's more secure. I'd only run PHP under nobody on a server with a small number of high-use users.
"Of course the real fix is to run phpsuexec and suexec. "
Yep, that's what I would suggest as well.
gotzaway, to enable PHP Suexec on your server, run /scripts/easyapache in a SSH session. Choose the "Advanced (Experts Only, At Your Own Risk)" option, and enable the 'PHP Suexec' option.
Alternately, you may do this via the 'Apache Update' option in WHM.