Forum Moderators: open
You need to check that there is not a creeping problem (ie. more and more pages going missing).
There are several recent (ish) threads on the subject so I should hunt them down. Penalties are one possibility, another is your host banning Googlebot, but there are several more explanations.
Kaled.
PS
If the site was down and the missing pages are static html, upload them again (or touch them to adjust file dates). There may be a problem with Googlebot's handling of if-modified-since requests.