I never used SEONuke, etc., but some one has linked to my site to reduce its ranking.
Has any used the Google Webmaster Disavow links tool with success?
Yes i've used it but without too much success so far. One tip is to make sure you use domain: instead of just the exact url that you want to disavow. That way, particularly for sites that use wordpress etc that have multiple pages, you'll disavow all the links on the domain.
I'm sure I read it takes about a month before you'd notice that anything's been cleaned up. I noticed this post is a little old so interested to see how you ended up?
Yea, I've used it many times with success on a bunch of sites.
It use to take long, G getting better with it. Sometimes it's easier to remove the actual link (if possible).
What kind of links are they? (web 2.0, bookmark, forum profile, etc.)
Had some friends afraid to use the tool because they thought it was some Google trap...nonsense in my opinion.
If you have a lot of authority links, those spammy links will not hurt you... From my own experience, it's better to invest time in creating new, powerful links than going out and try to remove those spammy links.