I would like to know the difference between link:example.com and webmaster tools back link checker. Which will give the effective result. I guess webmaster tools. If What is the exact reason for that? please clarify.
[edited by: tedster at 6:11 am (utc) on Mar. 27, 2009] [edit reason] switch to example.com - it cannot be owned [/edit]
You're correct that Webmaster Tools is a more complete report - even though it still does not show all backlinks. One of the big reasons is that Webmaster Tools is only seen by those who can verify that they are associated with the domain, the owners and their designated agents.
The link: operator on the other hand exposes its data to anyone - including your competition and others who may not have the best intentions towards your site.
Also, since anyone can access the link: operator data, it opens up the possibility of people scraping large quantities of Google's link data. If it was more than the mere sampling that is currently offered, such scraped data could be quite a tool for more precise reverse engineering of the algo, exposing Google results to more spam schemes. Some search engines (Ask, for instance) do not even show ANY of their backlink data.
You'll notice that not only are the link: operator results quite partial in Google, they also shift from time to time, sometimes dramatically.