Don't know if this could have anything to do with it but I've heard thyroid and adrenal issues can make your pupils do funky things.

http://www.medhelp.org/posts/Thyroid-Disorders/Low-Free-T3/show/17247

I've heard autoimmune diseases can cause adrenal fatigue, though I think a lot of drs think adrenal fatigue is kind of made up. You might want to see and endocrinologist and/or get your hormone levels checked.

Thank you very much for your reply Brian, this whole thing is freaking me out and I was really happy to see a response to my post. :-) I did more looking around online this morning and I found this stuff.

hippus /hippus/ (hipus) abnormal exaggeration of the rhythmic contraction and dilation of the pupil, independent of changes in illumination or in fixation of the eyes.

hippus
Small rhythmic variations in the size of the pupils. They are present in everybody and increase slightly at high luminances. The frequency of these oscillations is about 1.4 Hz. Hippus may also be associated with systemic disorders such as multiple sclerosis, neurosyphilis and myasthenia gravis.
http://medical-dictionary.thefreedictionary.com/hippus

I watched a video of some girl's eyes with hippus and it looks just like what mine are doing minus the flashlight. If anybody is interested in watching it, here is the link.
http://video.search.yahoo.com/search/video;_ylt=A0oG7njv9K5MnlIAeVtXNyoA?ei=UTF-8&p=hippus&fr2=tab-web&fr=ytff1-msgr

I couldn't find very much good information about it, which is frustrating. Has anyone ever heard about this before or know a good online resource?

Sounds like the muscles of the iris cause this. I would try taking magnesium or at least talk to your doctor and also ask him about magnesium. It orchestrates hundreds of activities in the body including helping transmit nerve signals. The reference is Carolyn Dean, MD, ND "The Miracle of Magnesium."

I just had this on Monday! Happened right after a nap, I felt my eyes spazzing out, the ocular muscles were spazzing and I opened my eyes and I had a nystagmus where my eyes were jerking back and forth really fast. I got to the bathroom as fast as I could because I wanted to see it. The nystagmus had stopped but my pupils were doing that. I was staying completely still and the light was exactly the same. I told my ophthalmologist about it and he said it was (DUH) something neurological...which is all I can get out of these good for nothing doctors. Thank you for posting this because everybody thinks I'm insane.