Originally Posted by JMac
there tends to be 50-100 from each domain linking to you.
That's probably the main issue right there. Frankly, it's just not that likely that a whole bunch of other independent websites would find 50 to 100 pages of any
site worthy of linking back to... and if they're linking 50 to 100 times to the same page on your site (say, the home page), it just looks even worse.
Since they're "nofollow," there's a good chance they're not passing any link juice back to you anyway (which means they weren't helping you all that much before) and they just make for an artificial-looking link profile (which means they could be hurting you now).
My advice: get rid of as many of the artificial-looking links as you can. You can then try filing a reinclusion request with Google. However, it's not a good idea to do that until you've made every effort to clean up your act.