I assume you are talking about the stick pens that are not retractable. We sometimes use them for stirrers, especially if Mr. B is cooking up some "lethal" concoction, like a mixture to be used on his plants. They can be stuck into pots or the ground to hold tags to identify the plants. Or you could color code the plants and not use tags, for instance, red for peppers, blue for carrots, etc.
If someone in your family has long hair, you could make hair ornaments that stick into updos or chignons. Just glue the ornament onto the pen and stick the pen through the bun or hair wrap.
Glue them onto bulletin boards or other decorations for a child's room or for your own writing room.
A lot of the retractable ones are refillable, but some may take specialty refills which you can find at an office supply store (not a discount store). I have several cheap ones or freebies that I refill simply because I like them.