Compare the environment when ran from the web to the environment when ran from the command line. Have your perl script print out the entire environment and look for differences.

You might find something like TNS_ADMIN is set in one, but not the other.

It sounds like you are already setting LD_LIBRARY_PATH, ORACLE_HOME, and ORACLE_SIDE -- but also make sure that your library files in the LD_LIBRARY_PATH have adequate permissions for the user who runs your Apache to access them.

Matt