Have you pulled off your back link reports from Google Webmaster Tools?
You should also run a complete backlink analysis using OSE, Majestic and another if you have one - drop them all into a sheet, removed dupes, and go through the sheet manually. You can often detect a toxic link quickly just by the url and anchor text. It can be a slow process but worthwhile.
You need to contact spammy sites and request they remove the offending links, otherwise you disavow them using the google tool.
That's the best way, I don't trust these auto apps to find toxix links. Remember that google still penalises manually which proves they still do manual work over automation.