Do you have any domains that don't seem to be indexed in Google? Maybe they were at one time, but then for some reason they were dropped. Maybe you have a site parked or a mini site with duplicate content. Maybe you're violating Google's Webmaster Guidelines. Perhaps you just purchased a name from some else and they were previously de-indexed for one reason or another. It's happened to me on more than one occasion. But what can you do?
Step one is to review your site to see what may have caused this. Usually, the reasons are obvious as outlined above. Once you've done that, you'll want to contact Google for reconsideration of your site. This is done by submitting a Reconsideration Request form at Google. But first, make sure you add and verify the site in your Google Webmaster Tools account.
When submitting the request, it's important to be honest and provide evidence of the situation and corrections you have made to the site. Let Google know if recently purchased the domain or if you have corrected issues, and include URLs where possible. These forms are reviewed by a team of actually people that will check your submission. Any dishonesty will get your request discarded.
I've heard reports of seeing improvements in a few days but in most cases it will be several weeks before you start to see improvements. Good luck, and let me know how it goes.