See,there are many factors of site deindexing. 1)Over optimization. 2)Keyword stuffing. 3)Useless content. 4) Illegally using image or wordpress themes. 5)Copied content 6)Wrong disclaimer 7)http error 8)Malware on your server. And many others factors...If you are sure that you have done everything perfect then leave a letter to Google about site reconsideration and have a deep breath for 1 MONTH..(Or more than that). Same thing happened to me.Complete site was deindexed by google due to some http errors and over optimization. After reconsideration it was back after 2months. Thanks.
Watch the video on this page, follow all tips, be very truthful, your banned so whats the point in hidding anything, if you fix it they will probably reindex you, takes about 3 weeks for a reply to say that they are now reviewing your site, when you get that it does not mean they have reindexed you yet, you may have to wait a further 3+ months before you see results, but you will have no idea about your status. Sucks but thats the facts. http://www.google.com/support/webmasters/bin/answer.py?hl=en&answer=35843
If your site has a lot of affiliate links and such they probably won't reindex you, at least they didn't for a couple of my sites, google doesn't like affiliate site. You could try getting some quality links from other sites, and see if they reindex you from those.
Submit your site to Google Webmasters if it isnt already and then submit a reinclusion request, stating that you have fixed any 'illegal SEO techniques' that you were doing. You have to be clear though and it will still take some time.
In some cases, a site could be de-indexed temporarily and will be re-indexed in few days or weeks after. Only a banned site will be permanently de-indexed.
Can you tell us why your site was de-indexed? Was it banned for some reason? If not, then may be your site is new? If yes, then you should simply wait and build some backlinks. New sites index and de-index quite often. If you think the site is banned, then you can submit a re-inclusion request in webmaster tools.
I got deindexed after having viruses in my Index page, it was like in iFrames though, I removed them, then waited around 3 weeks until they re-indexed my page, kind of annoying.