Google bills the Google Mini as a search appliance that’s able to deliver “the same reliable results you expect from Google web search” to your intranet or public website. I think Google is being misleading here, confusing their customer base into mistakenly believing they will receive the “same results” from the Google Mini as the Google.com web search. Google.com has major points of difference from the Google Mini. For example, Google.com takes numerous spam signals into account when determining indexation and rankings; Google Mini does not scan for the same spam signals. Google.com takes into account the PageRank scores of all inbound links; Google Mini does not.

As discovered by Joel on Software, the Mini never phones home, even to get public PageRank information; the search results it produces are entirely based on whatever documents you told it to crawl.

So, if your site’s PageRank is too low once you get into deep pages, then Googlebot may lose interest and may not even index the page, whereas Google Mini would be much more inclusive.

Or if a site contains something that looks dodgy — like noscript, noframes, hidden divs, tiny text, etc. — it will be a turn-off for Googlebot but not for Google Mini.

Thus, if you’re a Google Mini customer and your site is well-indexed, don’t take that to mean that your site will be well-indexed by Googlebot.