According to Matt Cutts, how much of your website gets indexed may well depend on the number of incoming links pointed to the site.
Quote:
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“Some folks that were doing a lot of reciprocal links might see less crawling. If your site has very few links where you’d be on the fringe of the crawl, then it’s relatively normal that changes in the crawl may change how much of your site we crawl. And if you’ve got an affiliate site, it makes sense to think about the amount of value-add that your site provides; you want to provide a reason why users would prefer your site.” Indexing Timeline
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