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Same here! Mind you when researching backlinks in the past, Yahoo was the place to go as they always showed more than Google.

Yes, and now Yahoo Site Explorer is off since Yahoo was acquired by Bing.
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Google webmaster tools comes up with about 70 links for one of my sites of which 50 or so are not listed (NO google sourced links listed) in the Spyglass results page.

They might not even be listed in Google publicly as well. We use the link: operator to extract backlinks from search engines, but Google shows only a tiny portion of links they're aware of:
http://www.youtube.com/watch?v=TjQ2QVQpaK0What you see in GWT is your OWN personal data, you can not get that data on your competitors, for instance. However if you wish you can transfer links from GWT to SEO SpyGlass (File -> New Project -> Expert options). Together with our database that generally gives out much more backlink data than Google, you can have a nearly complete backlink profile of your site.
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There are, of course, a lot of results in Spyglass that Google has not displayed - but thats not really the issue.

Some of the backlinks that Google lists can be found first in other sources, e.g. Alexa, Blekko, or SEO SpyGlass database - then they won't be indicated as "found in Google".