Try a search for your brand name, or domain in google. If you do not come up in the first position for that, then you have probably been blacklisted. Also do a search for site:yourdomain.com to see how many pages they have indexed for you.
If it looks like you are being penalised then submit a reinclusion request through webmaster central and they should review your site and reindex if you have removed any black hat
seo.