I've pretty much always used Google queries to evaluate backlinks. MSN and Yahoo! results were just never as helpful as Google's. The Google "link:" query has been "broken" for some time and doesn't return reliable results. Instead, I've relied on "www.mysite.com" -site:www.mysite.com, which shows you all links pointing to your site that are not on your site.

I recently started playing with Yahoo! Site Explorer to evaluate backlinks and I'm finding the results are better than Google's.  Using the tool is simple: enter your URL, then on the results page click "Inlinks", then from the drop down menu choose "Except from this domain". Compare these results for phpdirectory.com: Google (32) | Yahoo! Site Explorer (156).

Also, note that you can download the results to a tab separated values (TSV) file. 

To learn more about Yahoo! Site Explorer, check out the Link Building Wiki. Developers will also want to have a look at the Site Explorer API. Lastly, if you'd like to start using this functionality right from your browser's toolbar, download my Yahoo! Site Explorer Mozilla Search Plugin.