I just responded to this exact question. Here's my answer and a link to that question:
Honestly, my advice would be to grab a list of your backlinks using both Google Webmaster Console as well as the OpenSiteExplorer and merge them into a spreadsheet and get rid of all the duplicates.
Next step would be to identify which of those links are spammy and you'd be better of having them removed. This is in my opinion the hardest part depending upon the volume of sites/links.
Then hire somebody to find email addresses of the websites where you want links removed. Finding something on the page and if nothing else, using whois. I would then send an email to each one of those contacts and in a quick short email, tell me the URL where the link is located and your site URL. Tell them to remove the link right away since you have received a Google Warning. I would imagine this taking care of a good portion of those links. I would send another email in a week and then again for a total of 2-4 times to see if you get a response and get the link removed. When nothing else worked, offer then $10 for the link removal and that should gain their attention. If that does not work either, I would suggest you move on.
I hope this helps. You could get somebody on odesk.com or a similar site to get all the labor intensive work done.