You can consider the following tools for your SEO Audit. Open Site Explorer Website Auditor Web CEO Alexa Site Audit Website Grader
If you are doing a general audit on your website I would recommend using WooRank like UDay11 said and WebsiteGrader by Hubspot which Alfie recommended. On top of that if you want to do an audit on your links and urls, try using Screaming Frog to get some good results. ~Nick B.
As of now, Opensiteexplorer.org, Woorank, MajesticSEO seems to be good. Though we cannot obtain complete results until we upgrade, it remains to be an effective one.