Search engines count links as votes of quality. They primarily want to count editorial links that were earned over links that were bought or bartered.
Many paid links, such as those from quality directories, still count as signs of votes as long as they are also associated with editorial quality standards. If they are from sites without editorial control, like link farms, they are not likely to help you rank well. Using an algorithm similar to TrustRank, some search engines may place more trust on well known sites with strong editorial guidelines.