If I have
http://www.site.com
And
<a href="http://www.site.com">www.site.com</a>
The second one is bad, but will the first one count as an out link?
If there is no HTML there is no link. So the second one is a link and has SEO value (it is counted as a "vote" and passes PageRank). The first only has SEO value as content, not as a link (just like any other text on your website).
Google has started to identify URLs that are shown as text on the page, as well as URLs that are embedded in javascript.
When it finds URLs like this, googlebot certainly now crawls them. It is unclear whether Google is also factoring them into the pagerank algorithm. (My opinion is that it does.)