It's hard to comment directly on your situation, as there are no concrete examples to look at, but a couple of thoughts:

In general, search engines tend to do a lot better with static HTML pages than they do with dynamic content. Form submissions, site searches, and other such user-friendly interfaces on dynamic sites cause real problems for crawlers. Many dynamic sites require user decisions to deliver content - these things are just not easily codeable from the crawler-side.

Part of Google's PageRank algorithm is dependent on how many links there are to a given page (from other sites). I'd guess that a lot of people with websites like Perlmonks. Not knowing a lot about PageRank, I'm guessing that the real difference in scores between PerlMonks content and your site's dynamic content has to do with the last point - external links. How to fix that? Get more people to link to you.

A company I worked for back in the dot-com days did a lot of crawling, and some sites were just impossible - javascript or search forms would be the only way to navigate the site, and you can't just clobber a search CGI to find what you're looking for. Our solution was to get these sites to send us DB dumps of the info we needed instead. Perhaps Google has a service like that available?