Create enough quality content to outrank the negative article.
By content I mean:
Video - distribute on youtube & other video sites
Articles - syndicate on ezineartcles, hubapges etc,
Blog posts - on wordpress, blogger, etc.
Slides & PDF - distribute on slideshare.net, dosctoc.com
* Bookmark all of the above on reddit, digg, delicious, etc
*Ping all of the above with pingler.com
* Build backlinks to all of them.
Make sure you target the exact same keywords for which the negative article is ranking.
Say your company is XYZ and there is a negative article titled XYZ scam ranking in the search engines;
target the same keyword XYZ scam with articles, blog posts, slides PDF explaining why your company is not a scam, using the methods I descibed above.