You can find out if your site has been identified as spreading malicious software ("badware") by checking the Summary page for the site in webmaster tools. (Note, you need to verify site ownership to see this information.)
This identification is determined by guidelines set by StopBadware.org If you feel your site has been mistakenly identified, or you make changes to your site so that it no longer spreads malicious software, you can request that your site be reviewed.
All appeals and reviews are handled by StopBadware.org. Please send an email to firstname.lastname@example.org explaining why you think your site was mistakenly identified or how you have modified your site. They will investigate and contact you with their findings. If they determine that your site does not spread malicious software, they will inform Google, who will remove the identification from the search results.