Happened to me this week. Usually, when your site is gone, better to be afraid of Google penaly due to using wrong techniques, like illegal link-building, hidden text, meta-data spamming etc. It's possible to check the reason out from Google Webmaster Tools page (first, you have to authorize the site monitored).
We made micro-site for a book, supporting traditional marketing channels. As usually, we did pay lot of attention to SEO-friendly design. Used WordPress engine, All-in-One SEO and Google integration plugins among others.
Google picked up our site in one week. Yes, it's painful time, but it's always slow, Can be up to 4 weeks, people talk in the net. Google indexed first pages, found keywords and Google search statistics started to build up. And then -- bah! No results anymore, nothing. Google entirely forgot about our site.
Like always, you start to blame yourself. Did I use correct skin? There are hidden links sometimes in "bad" skins. As our skin was downloaded from Wordpress official site, it was OK. No hidden text etc hound from the code. Secondly, did We liknk to "bad" websites. No, we didn't. May-be some of our comments has bad link, no, checked. Some AdWord campaigns unpaid, overdue to Google? Checked, negative! We also checked html quality, missing pages and other such thing. Everything seemed to be OK.
No solution, Our site just re-appeared in 2-3 days slowly back to search results, like newly discovered site. No correct explanation found. It's good now.
It's always good to keep regularly. at least weekly, eye on your site Google-performance. Ask site:www.yoursite.com , check keyword positions etc. Otherwise can happen, whes one of our site was down 2 weeks cause of black-hat SEO used in the code...