tedster - 10:04 pm on Apr 17, 2010 (gmt 0)
Google has never said that they list "all" links that point to a url - the list has always and only been a sampling. The sampling is fuller within Webmaster Tools than it is in the public site: operator. But it has never been complete, and likely will never be complete either, because that would allow very aggressive reverse engineering of the SERPs.
Some search engines - Ask.com for example - don't even report links at all. I think the Ask algorithm is VERY heavily dependent on link neighborhoods and that's why they protect their link data so intensely.