If every single link to a given website www.example.com points to a page in a particular subdirectory (i.e. www.example.com/user/[something]), but that directory is off limits as per robots.txt, i.e.User-agent: *Disallow: /user/because I don't want these pages appearing in google search results, am I shooting myself in the foot in terms of pagerank? Does the incoming link-juice still count if the target page is forbidden to Google in my robots.txt?
PageRank: will links pointing to pages protected by robots.txt still count?
google;pagerank;robots.txt
Speaking to your question - Does the incoming 'link-juice' still count if the target page is forbidden to Google in my robots.txt? - I would say that PageRank is calculated, even for noindex/nofollow URI's:While Google won't crawl or index the  content of pages blocked by  robots.txt, we may still index the  URLs if we find them on other pages on  the web. As a result, the URL of the  page and, potentially, other publicly  available information such as anchor  text in links to the site, or the  title from the Open Directory Project,  can appear in Google search results.Google Webmaster Central: Block or remove pages using a robots.txt fileExample: My working-model.com domain has had an all-exclusive robots.txt specified for as long as I can remember, however, a Google search for working-model.com (or a Yahoo search, or a Bing search) shows a rank for the domain (probably as a result of a domain WHOIS site linking in).