Is this running under mod_perl (Apache::Registry,etc)?
You say CGI, but I thought I'd ask anyway. In my experience, it's odd to leak a lot of memory under CGI (maybe I'm just lucky). Under mod_perl, if your not careful it's likely. You could always try setting MaxRequestsPerChild lower to try and contain the problem in the meanwhile.
Also persistant data storage such as caching of database handles in Apache::DBI, Statements using DBIs prepare_chached and cached templates in HTML::Template