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If the site is doing well, avoid panicking - lots of webmasters freak out and go on a rampage trying to remove every link, when they should just sit back and relax. If we're talking thousands and thousands of junk comments, it's something you might want to be concerned about. If it's a lower number, I wouldn't lose too much sleep over it and would focus on building quality backlinks going forward. Contacting blog owners is a nightmarish task because the sort who have blogs that auto-approve junk comments are usually not the most tech-savvy and often don't even think to include their contact info anywhere. Lots of them don't own their own domain, so you can't get their whois info that way either. If it were me, I'd put my time and energy into building good, diverse backlinks rather than spending tons of time trying to remove these links that don't seem to have negatively affected you.

Are you sure these links are actually hurting your site? A lot of people think their site is being penalized when it actually isn't. If we're talking just a few links from lousy sites, it's probably not hurting your site. If we're talking a large scale thing though, it could have a negative effect.

Your best bet is to try to have the links actually removed from the spammy sites. If that fails, that's where the disavow tool comes in, but it can potentially take quite a long time to see any changes

It also sounds to me like you are expecting to see results from using the disavow tool too quickly. According to Google the disavow tool should be used with caution and only by those who absolutely know they need it. Results will not be instant and it can take several weeks or even months for some sites to recover, and recovery is often not to the point it was at prior to being hit. How did you determine that your site was being penalized?

The number of links that show up in webmaster tools is not an exact carbon copy of the links Google considers when figuring out where to rank your site. Google is typically aware of A LOT more links to your site than just the ones which show up on the webmaster tools list & I wouldn't put too much stock in the number you find there. Google is not going to show you their whole deck of cards, unfortunately. That's why sites like Open Site Explorer are awesome for finding all the links that webmaster tools doesn't show.

I would also advise that you focus more attention on your site itself rather than just its backlink profile. Work on developing quality content that people want to link to & develop your social networking presence on Twitter, FB, G+, Pinterest etc... Ideally, you want your visitors to be the ones sharing your links and content, so make sure your content is interesting.