If a directory has a google page rank of say 5, and if I get my site listed in that directory, my listing is not on the front page, it is on a page that has a page rank of 0. So how does that work in terms of link juice? Does google still recognize that the link is from a page rank 5 site, even though my link is not on a page with a rank of 5?
Yes, your site would be on 0 page rank or na page rank, it doesn't mean that if directory home page is pr5 then your link would be placed on PR 5. But after some month the pages pr may increase then you can get benefit of..