When Google is evaluating your inbound links and relativity for SERP, do they factor in the links that are coming from subpages? So, in theory is it better to have site wide links on high PR sites that don't have a lot of outbound links? Or is it better to have links coming from multiple home pages that are high PR and not be concerned with the value of the subpages?

Google takes all links into account. Each webpage carries some link value, be it the homepage or a subpage. So you can get links from subpages and, when you get a chance, get links from homepages as well.

A site-wide link, however, is not the best idea, because often Google considers site-wide links paid ones and devalues them to some extent.

but if it is a site wide link on a totally relevant subject wouldn't that be okay? I am just trying to figure out how to get a lot of link power and so we have been looking for sites that are relevant that don't have a lot of outbound links throughout the site and then we are adding sitewide links. You saying it is better to try to pick and choose only specific pages that have high link value?

There is such an opinion, yes. Most probably Google's logic is: normally a webmaster would link to an interesting resource once from a certain page or several times from several other pages, but he won't be normally putting a link to an interesting site into header/footer to make it a sitewide link.

I see your point, but if that site wide link is on a very relevant site and there are lots of clicks coming from that site to your site, I think Google would see it as relevant and hopefully not penalize me. I noticed a lot of our competitors are doing it, so that is why we are trying to do it now.

Sure, it's worth giving it a try, especially if there's traffic involved, not only SEO link value. After all it's best to check all the advice in practice as the rules are very flexible.