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Building up link juice takes a long time. Replacing your current negative link profile with a positive one will take a long time as well.
The first thing to do is remove reciprocal links to any questionable neighborhoods. That may help some.
Other than that, focus on building a strong link profile. If you haven't already, consider submitting to the high-end, human reviewed website directories. Yahoo, Business.com and MSN SBD are the big three. Yeah, they cost money, but there are good links for Google.
Write some quality articles about your industry and submit them to your industry's websites in exchange for a link. Don't submit these everywhere, or use automated submission services as you may make your link profile worse.
Engage with some of the bloggers in your industry. Contribute quality comments to their blogs, and, as they get to know you, see if they'll talk about your site. Don't overreach on this. Cory Doctorow isn't going to profile you on Boing Boing unless you're doing something very cool.
Create tools/resources for your industry. Make them better than anything that is already out there. Let other industry sites know about them.
That's just a few things off the top of my head.
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