Have you tried building some web2.0 micro sites, social bookmarking, relational forum contribution and blog commenting???
Also take a look at your competitors... where are THEY getting their backlinks from?
As highlighted I think quality is definitely a major factor. Directories have definitely not carried as much weight as they used to (due to the over saturation of the directory industry).
As with any link building technique quality and variety are key, so if you are going to build directory...
Social bookmarks definitely won't generate a negative effect on your rankings, in fact its a great way of getting your site indexed initially (due to the crawl rate of such sites).
Are you sure your site has been penalized or perhaps your site is just rather new and is yet to rank in the SERPs?
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