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While that's still true, I've recently seen some pretty extreme discrepencies between what Yahoo reports (for example 3,200) and what Google reports (same example, 2). Looks to me like something even crazier than usual is going on with the link: operator.
At any rate, I never look to Google for anything like accurate and complete information on your backlinks. They usually know about almost all of them, but they're not talking, at least not in public.
Whilst doing research I found a link to a site containing some useful data, it was like site.com/dir1/dir2/0.html. It was a plaintext file in html. Some of the data was missing, so I figured it would be on another page. I tried manually entering in 1.html but it was a different set of data... I tried browsing the top directory but permission denied. So where was the missing data I needed to find!?
I thought I will use the google link command, to see what page on their site links to the data set - I figured it would contain links to the other sets of data. The link: command turned up nothing. Not even the site I followed the link from.
Just thought I would share this; it was a valid use of the link command, and because google filter the command I could not find the information I was looking for. Isn't google's aim to organise the world's information!?
Anyway, it's the first time I have been unhappy with google's service out of its entire time of operation so I'm not complaining!.