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Taking this on board - As far as I know (and someone correct me if I'm wrong), but Googlebot in particular reads the first 101k of a site only. Therefore all Javascript code should be held in an external file, or at the bottom of the webpage.
I don't know off the top of my head the page size limits of any other spiders.
if a site has a whole lot of javascript pop-up windows containing keywords, etc., then Googlebot and other spiders won't find them because the links are javascript - i.e. they should be re-done as html links?
Create a sitemap page and ensure there are links to these pages,
or
Change your links to standard html links.
is the 101K limit for Googlebot for the entire site, or per each unique page on the site?
JP