I was trying to increase the number of open files allowed for a user on a Debian 5 box. Changing /etc/security/limits.conf was being ignored until I added the following line to /etc/pam.d/common-session.
session required pam_limits.so
Logging out and in again after adding that line gave the new session the ulimit I was trying to configure.
Took quite a lot of googling to find this: http://www.zimbra.com/forums/administrators/16066-solved-too-many-open-files-error.html
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