Considering the Monistary as an Example... I would go with mod_perl. I would write a simple template system, perhaps a normal Perl module called Monistary::Template and use that for all my page formatting needs.

I would then go on to build the mod_perl modules. One (that get's pre loaded when the httpd server starts) would be called Monistary::Nodes that would handle all the node retrieval.

Next would be things like Monistary::SeekersOfWisdom... but then again, do we really need a module for each section? I'm not too sure we do since everything is a node, after all.

Better idea IMHO would be to write Monistary (aka. Monistary.pm)

Using apache, Monistary would govern everything about the site as follows:

<Location />
  SetHandler perl-script
  PerlHandler Monistary
</ Location>

According to the way everything seems to be handled by index.pl here, I think mod_perl isn't in use, at least the way I'm suggesting.

As for HTML handling? I'd go with the aformentioned template system... there are some great modules already in existence to subclass and take advantage of. Enjoy!

--
Casey