As much as I think site explorer is a great idea, in practice, it's still not as useful as Yahoo!'s normal linkdomain command. There are some fantastic features in there that I use all the time, for example:

1. Removing sites from the list as in a search for linkdomain:seomoz.org -site:seomoz.org (note that you can use this to remove multiple site if you have a few sitewides dominating the results)
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2. Searching only a particular site for links as in linkdomain:seomoz.org site:blogspot.com
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3. Using specific terms when searching as in linkdomain:seomoz.org msn interview (this can be particularly useful if you want to see whether your links are from generally on topic pages or to roughly check anchor text)
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4. Using specific terms, as above, to check for the presence of competitors on those link pages as in linkdomain:seomoz.org seobook.com (note that I don't use site:, just the term)
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5. Using specific terms to see how many links come from a forum or blog as in linkdomain:seomoz.org thread reply forum (this won't show you all the links unless you click the "show more results" at the end)
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6. Speaking of the "end" of Yahoo's results, going to page 999 on a linkdomain search can be very revealing. For example, for a site like wikipedia.org, the 999th page shows some real, valuable links from real pages - that's telling me that Wikipedia really has that many valuable, high quality links. The reason I can ascertain that is by looking at what the 999th page usually looks like for sites like online-poker.com (I just made that up, so I hope it doesn't belong to someone here) or even our client Avatar (who has mostly spammy scrapers listed at that level).

Linkdomain is a powerful command and its uses are even more varied than those I've listed above. Try for yourself and see what you can find - there's no better source of link information currently available on the web.