I was asked why Google does not display all of ones backlinks when doing the link: query on the SEO Radio show last Tuesday. I really did not have an answer, but it makes for a good topic. I did some forum searching and scavenging and found an interesting post.
At WebmasterWorld, GoogleGuy in msg # 10 says:
What I was trying to say earlier was that it would be good for smaller web sites (e.g. Mom and Pop sites that might not have tons of backlinks with a PageRank of 4 or higher) to be able to see some of their backlinks. There's a lot of interesting ways to show summary stats from a graph like web linkage, and I can see where a site that has backlinks with lower PageRank might want to see a few of their links as well.
In my experience, folks make two main mistakes about the backlinks we export. First, when they don't see a backlink in response to link: queries, they assume that link isn't counting. The fact is that internally we have complete copies of links we saw, but just don't show them all. The other mistake is to assume that just because we show a link in response to link: queries that it somehow counts more. Honestly, I wouldn't read that much into whether a particular link shows up in response to a link: command.
So why do they show link from page A but not from page B? Still no answer. But as I ventured to guess on the SEO Radio show, maybe Google doesn't want you to know some much about your "natural link" count. I'll stop there, you get my point.