This seems to be a frequently asked question, so a bit of googlesearching or supersearching here should give you some insights.

Take a look at how http://www.slashcode.org and http://www.openinteract.org structure their "web applications", as two large-scaling mod_perl applications do the trick. Both perhaps coincidentally are layered with Template Toolkit.

-- Randal L. Schwartz, Perl hacker
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