Great question.  I've been wondering about that myself, as I also noticed big backlink discrepancies in WMT - my numbers climbed quickly as I signed up for Google Authorship from 6,000 backlinks to 21,000 backlinks within a few weeks, but then suddenly started dropping again.  Right now I'm hovering around the 16,000 mark and can't figure out why.  Someone suggested using  http://siteexplorer.info - not sure how good it is but may be worth checking out.

Google Webmaster Tools will only give you a sample of your overall link profile. It is a good place to start but it is not ever going to be a complete view of the links you have. I would not worry if links have dissapeared as it happens from time to time. As an example below with the different methods you can use to check links, well some common methods at that: 1. Using the syntax "link:www.website.com" - this will show a small number of links, I would not advise on using it. 2. Using "www.website.com" in google search to view links - this will show more links. 3. Using Webmaster tools - this will show more, but it is not complete. 4. Using Open Site Explorer from SEOmoz - This will show more links but the crawl delay is around 1 month so links take a while to show. 5. Using Tools like Majestic SEO and Ahrefs - these tools will be more advanced in the way they show backlinks they both cost between 100-200 a month to run but they will show a more complete backlink profile. 6. Many people also build custom tools to check links when they are built and how active they are too that is another more advanced option. I hope this helps.

Thanks for the detailed response James. I looked at SEOMoz before and a few other web based backlink checker and it shows the links - i was more concerned for indexing purposes and domain authority that WMT wasn't picking it up.

Great help