A few sign: 1. Ranking drop. 2. Check: site:yourdomain.com on Google if not available than your site has been de-indexed.
My site has not been de-indexed, but the ranking has dropped. From what I have read, Google issues demerits based on "what they consider" spam backlinks. Do they issue any notification, or give you any way to check and see if your drop was because of this or because other sites have just improved?
Try signing into the Google Webmaster tools. They'll alert you to a bunch of info on your site and links. It won't necessarily indicate which backlinks are hurting your site, but it can help to take a look.
With this search i.e. site:yourdomain.com you would also be able to see all the pages are indexed in search engines.