from www.peteducation.com (companion to Drs. Foster and Smith's Web site):

Description: Benign growths of hard tissue which look like small horns; cause unknown, though may be associated with some underlying disease such as cancers, follicular cysts, or FeLV
Symptoms: ½ to 2 inch hard horn-like growths; may be single or multiple; in cats may occur on foot pads
Diagnosis: Clinical appearance; look for underlying cause
Treatment: Surgical removal

from www.vetinfo.com:

There are a number of suspected underlying causes for cutaneous horn formation on cat footpads or other areas (sometimes these occur on the face or other areas). In our practice, though, we see a lot of these that we can't find any underlying cause for. Among the known underlying causes are squamous cell carcinoma, a form of cancer, and the reason that a biopsy was probably done. Fortunately, that doesn't appear to have been the cause. More commonly, these are linked to feline leukemia virus or feline immunodeficiency virus infection, although lots of cats are negative for both of these viruses when the cutaneous horns are found, as well, just like yours.

When no underlying cause can be found it is OK just to trim these down to the level of the footpad when they start to bother the cat. These usually don't have a blood supply and it is possible to trim them using a nail trimmer without causing pain (or at least not apparent pain). Some people use keratolytic solutions, such as Kerasolve (tm) to dissolve these but we haven't tried this since we have good luck just trimming the horns and since cats tend to lick ointments or solutions off their feet.

I do think it would be a good idea to watch carefully for signs of a more severe problem, such as a tumor, developing at or near the site of the cutaneous horns but the odds of this happening are pretty low.

It is entirely possible that some day a viral underlying cause will be identified since a lot of vets seem to think that a virus is the most likely culprit as a cause of this problem.