Mod_rewrite defiantly makes a huge difference to database driven sites on the engines (especially Google).
As far as LinksSQL is concerned the problem lies with using Perl for dynamic pages, Google will index these pages (even with a variable in the URL) example: http://126.96.36.199/search?q=cache:http%3A%2F%2Fwww.bestflashanimationsite.com%2Fcgi-bin%2Freview.cgi%3FID%3D599
but on the whole they avoid it (due to the load it can place on a server) more so than middleware pages like PHP, ASP, CFM etc. that use query strings.
There's a good article here about 3 methods for seting up search engine friendly URLs:
Comedy Quotes - Glinks 3.3.0, PageBuilder, StaticURLtr, CAPTCHA, User_Edit_Profile