In the June 2002 issue of Linux Journal there is an article titled, "BestCrypt: Cross-Platform Filesystem Encryption". It reviews the BestCrypt software (free for non-commercial use, reasonably priced for commercial use). From the article, it sounds like a possible solution to your problem.

However, experience has taught me that the sysadmin who supports the server will have a say in what is installed, etc. Consult her/him on the subject when evaluating solutions.