As long as you use unique titles and descriptions, the chances of a penalty are greatly reduced. Also, try submitting to directories that don't get a lot of submissions regularly. Here is a list that I use which you may find useful:
https://www.directory.express/
http://www.kizex.com/
https://www.ayroo.com/
http://www.rowma.com/
http://www.wayry.com/
https://www.linkvertex.com/
https://www.ultimatedir.com/
Again, make sure you always use unique titles and descriptions as much as possible. And if you are trying to rank for a certain phrase, spin it with different words.
For example, if you wanted to rank for "Directory List", you would use titles like: "Best Directory List", "General Directory List", and so on.
