Google only shows you a sample of links to your site. They do not show you all links pointing towards your site.
To confirm, search for your domain-name in various search engines. Using "quotation marks" around your domain name helps.
Link checkers or link popularity checks (see below for example) will show you all existing links pointing towards your site. Link checkers count links leading to your site from multiple search engines. The exception is the links from Google. Links from Google are sampled, but not listed exhaustively.
The reason is that Google doea not want you to know this information exactly. Presumably this is because the idea behind Google is a system to utilise, but not to try & overtly influence.
take a look at the useful links thread:
http://www.opentracker.net/forum/viewtopic.php?t=6
where you will find this link checker listed:
http://www.marketleap.com/publinkpop