Do you believe Google webmaster tools or yahoo site explore for an accurate number of index back links... I get different numbers for all of my sites...
Yahoo would be a more complete list of website linking to your site... however google is likely more relevant. Google doesn't count all links only the ones they deem to be relevant / quality links.
I prefer using google webmaster tools. I can see backlinks for each page using filters. niceilike, I think you are referring to 'link:domain.tld' query when you say only relevant links are included (though I would disagree with that too )
For the link quantity, google is more accurate after it updates its webmaster tools . I can see all my sig links in webmaster tools .