I normally use .php includes function and know Googlebot crawls it fine, but my question is if you use a different way that isn't php, say SSI with a text file that you have your links in will Googlebot read that?
you can use asp as well and googlebot will cache it just fine. i am not sure aboyt jsp. i dont use jsp so i can not give you a sure answer about it.
Search engines are interested in the final content - they do not really care what you used to produce the final result. So, yes - googlebot will read your links if you use SSI, php, ASP etc... The only way to tell what was used to produce the resulting content is to look at the file extension like .php or .ask and presume that was used to create the output - you can hide this fact by creating a search engine friendly urls in .htaccess and script your site accordingly
My understanding is that SEs don't like when the php or asp URL has a "?" in it pulling in an "id". Is this true?