Hi Spry, as you already mentioned, not all links has the same weight, there are navigationla links like in the footer, in the menu; also google may give some different weight among them, moreover some value may be reduced, and also there are some other factors that google uses to weight each link in a page that we don't know, but we may assume they have.
So given that we can calculate an aproximate value of juice passed from a link to another I won't rely so much in PR, the time you're spending in this caluclations may be given to other tasks. In general you may assume that the best pages to obtain links are pages which are nearest to the homepage of a site and which has the least number of outgoing (both internal and external) links.
Don't rely so much on PR, I've seen so many low page rank pages ranking well and high pr pages with no rankings that I think that you need to consider other parameters which are more important when it comes to linkbuilding: age of the domain, authority, topic related, etc etc.
If your calculations are made for onsite optimization just try to have your main pages higher in your site structure and linked directly from the homepage or from m ain categories.