Hybrid pen will help you on a champ that you are going to be using both types of damage. So someone who either has a lot of both physical and magic damage, or when you have a champion that is AP, but that you will be weaving in a lot of auto attacks. A good example is someone like Sona. Who is a mage, with AP scalings on her abilities, but her passive allows for additional magic damage on her next auto attack (for her q specifically). So taking hybrid pen runes on her makes her passive more effective.
Some people used to like to use them on Akali pre-rework, though I do not know if that is still the case now. I don't actually play her.
You would not necessarily want hybrid pen on Lissandra as her auto attacks are a very minor component of her overall damage output. You want either AP marks, or Magic Pen marks. Ryze, I am not certain of, as I have not played him since his rework, but he still seems to be based around spell-spamming, which would indicate the same as Lissandra, AP or Magic Pen.