Yes, previous to Penguin 4, links from low-quality directories and bookmarking sites was viewed as a negative ranking factor.

“Here are a few common examples of unnatural links that may violate our guidelines: Low-quality directory or bookmark site links” source

Gone are the days when one could improve rankings by getting links from thousands of directories and bookmarking websites. This tactic not only doesn’t work but in the past, it could also get your site penalized. Thanks to Penguin 4, now links from such sites are rather (mostly) devalued.