CGI/Mod Perl Application Design philosophy - which way do we go? is a pretty good thread about this kind of thing. I'd normally recommend OpenInteract (as some other kind folks have mentioned), but it does not currently run under a CGI environment, just mod_perl. CGI/standalone/POE/... is in the future, but not yet.
I don't think anyone else has mentioned it yet, but OpenFrame is pretty nifty and IIRC runs under CGI no problem.
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