I spent some time going through my logs and comparing the list of links that Google has indexed for my site in Webmaster Tools against the sites that pass me traffic through links. The differences between the two lists are huge and some of the links are links I would definitely like to have indexed.
I'm just wondering how I should go about getting some of these not indexed links indexed by Google. I don't want to point links from my site to these links as they would now change from being natural one way links to being reciprocal links. I'm not talking about getting 600 links indexed, but maybe the top 10% quality wise.
I have ideas on how to tackle this, but I'm interested in what other people think.
It is my understanding that the list of external links shown in Webmaster Tools is not comprehensive. I discovered this when my links dropped by 30% on one crawl, and then came back the next time they crawled. Checking the exact wording, Google doesn't claim that it is a comprehensive list (though we know it's a lot more comprehensive than the link: command). So don't worry about this too much. If the link is there, Google will find it and take it into consideration in the SERPs.