For starters, you should refer to the following Wikipedia entry for "Deep Web"; http://en.wikipedia.org/wiki/Deep_web
[extract]
The deep Web (or Deepnet, invisible Web or hidden Web) refers to World Wide Web content not part of the surface Web indexed by search engines.
This phenomenon is also sometimes referred to as "dark matter". It's a result of the fact, that [search engine] "spiders" or "robots" (or "spider bots") are unable to crawl, or access -- in order to index -- [certain] content; usually content that is generated dynamically. The following article explains more;
The Invisible Web Revealed
http://www.robertlackie.com/invisible/index.html
Your question dealt with languages. PHP, JavaScript, content returned via the CGI mechanism -- where languages such as Perl, Python, and even C are common -- can all conceivably "jam" a search engine bot. If you wish to implement your site using -- ideally, "well formed" -- HTML exclusively, then you can pretty much count on the fact that search engines will have no problem whatsoever, indexing the full content of your site.