The site command (site:www.domain.com) is often used to determine the health of a web site in a search engine. The thing is, Google's site command is far from accurate and too many SEOs look at it too closely. We discussed this before and I just want to cover it again.
Googler, JohnMu, said in a Google Webmaster Help thread:
Focusing on the site:-query rough approximations will not lead to useful results.
Did he just say that the site command results are not useful? Are you surprised? I'm not. Like I said, we said this before.
For example, a site:www.seroundtable.com command returns for me over 17,000 pages. When I look at Google Webmaster Tools, I see indexed URLs at 9,921. So who do I believe?
We discussed the site command dozens of times here over the course of about 6 years. It is interesting to see how this has changed over the years.
Forum discussion at Google Webmaster Help.

Comments:
Michael Martinez
07/15/2009 05:18 pm
LOL! So we're supposed to trust the information provided by Webmaster Tools rather than what we find in the search results. Nice conundrum, Google. Maybe you should fix one or the other and then start advising people where to look for information about how many pages are indexed.
Aloysius Carl
07/15/2009 07:47 pm
From what I have seen the supplemental pages are in the site: search results, but Google does not include them in the counts for indexed pages in the Webmaster tools. And no surprises here ... we still use the site search as a gauge of the potential pages to push into the index
seoz87
07/16/2009 03:46 am
no link: command, no site: command...do wee need to hack into someone's web-master central account to see the stats for a website :s
Rob Abdul
07/16/2009 07:59 am
By the way to contrast this with Yahoo’s offerings; their Site Explorer is amazingly accurate. Use that I say.
Pradeep Ehan
10/26/2010 04:46 pm
Site: Command is work independent, If you command with site:www.yourdomain.com which is finding the all pages in your req. the qoury is show you all pages, some time your pages there no SEO frindly URL or Title. Then Goolgle undersanad that proposal is the same.