Isn't the site:website.com command supposed to list all indexed Pages? I've got the feeling that it only lists a fraction of what they really have indexed.
site:domain.com shows the number of pages that google knows (main + supplemental index) site:domain.com/* just main index site:domain.com -site:domain.com/* just supplemental index
Using the three methods above: site:website.com/* = 32 site:website.com = 482 allinurl:domain.com/ = 22000
Have you seen this? Which can be seen on the very last result page when you're checking a site command. Google excludes some of the indexed pages if they find those page similar to what has already been shown in the results. Then again, you can still have the list shown by clicking on the "repeat the search with the omitted results included" link.
Googe naturally limit showing indexes and backlinks they've gathered for all sites.. may be for reason of competition so competitors can't easily or totally duplicate the structure or contents of the site... and they can't easily get the total number of site's backlinks and where they came from..