Footer and boilerplate content have been discussed and covered quite a lot but it seems that we have to mention them again. The man responsible for that is John Mueller as he again brought the topic up while answering a question in a Google Hangout. This happened on the 15th of April on Google+.
According to his words, Google will not penalize you if you have footer or boilerplate content and links. The confusion probably comes from the fact they these types of blocks are not understood and addressed as primary content by Google. John added an example to make things more clear:
So for example, if you have to put a legal disclaimer on your footer of your web site for legal reasons. That doesn’t mean the rest of the content on those pages will be devalued. But rather, we will try to figure out, oh this is disclaimer that is across the site, so that if someone is specifically looking for this disclaimer, fine, we will show one of the pages from the site, but otherwise we won’t treat it as primary content for that page.
In general, you will not get penalized by Google for having links in your footer because they are not seen as that important by the search engine.