I run a few Instiki sites on Phusion Passenger, and they occasionally break – namely, they give a ‘Permission denied’ message which is hard to track.
The problem is that there are temp files like /tmp/passenger.1234 which have some kind of permissions problem.
To resolve this, you can simply delete those files, like with:
sudo rm -r /tmp/passenger*
and reboot Instiki (Apache, really):
sudo apachectl graceful