Hi everyone, just wanted to give an update on this situation with some more information:
* Site was updated across the board about 3 weeks ago
* Just homepage is not showing up in SERPS, other nested pages are showing up for their targeted keywords
* Homepage is cached, I can see it when I perform a "site:" command
* Homepage shows 20th June 2010 as its last cache date
* I cannot see homepage in results even when I go to "omitted results"
* I can see another page in the domain ranking on page 5 for one of the main keywords - this must mean that it is allowing us to compete for the main keywords but that the homepage is not allowed
From the data it seems clear that just the homepage (which has the highest PR and competes for the main terms) is completely missing from the SERPS. The only search I can do to bring up the homepage in the results is if I search for our actual domain name.
My conclusion on the situation is that we have tripped some flag or filter and have been temporarily removed - it's just odd that it is only the homepage that has been removed. Another possibility was that we have aquired too many incoming links with similar anchor text to the homepage, but it seems odd timing that it is around a major update. And too many similar incoming links should flag us for keywords rather than having the page removed from the index I would imagine.
Given the health of other SEO aspects I think that it is nothing to worry about and the page will return over time. Any contrary arguments would be very welcome though!