Unlike other comments I do believe that search engines may take page type into account. There was a long period for example where SEs(Search Engines) would not index URLs with parameters in them at all. Google was one of the first ones I noticed actually following links such as these. I have noticed that people who administer discussion forums complain that many of their "guests" are actually SE spiders. I felt my rankings rose when I switched from pages with parameters to more normal "looking" .shtml pages.
Search Engine Optimisation is a whole topic of its own so I will not ramble forever and instead will point you to Webmaster World
where there is an amazing accumulation of knowledge from people who are keep up with the day to day details of search engine ranking algorithms. I hope you will find much interesting reading there - I know I did.
Of course, you don't need to have all your perl cgi scripts end with .pl there is more than one way to do this ranging from simply renaming them to using mod_rewrite to make your CGI scripts look like static page URLs. Mod_rewrite is especially handy if you have a set of scripts in place already and don't want to change them all.