Removed links we could remove, and contacted webmasters to help us removing (suspicious links)
Recreated the whole site, with a new backend, enhanced page speed
Created new content (taking into account what users are and were looking for)
De-optimized what we considered over-optimized SEO
Tried to build new (clean and not black-hat) external links
Improved our Social sites (facebook, twitter, opened a pinterest account)
Corrected the errors reported in Google Webmaster Tools (as much as we could)
Etc, and other things