Can't know for sure without an MRI, but a popping knee is often the sign of a torn meniscus. A flap of connective tissue may have torn loose and gets trapped between the two articulating surfaces as you pedal. If it's not painful, you can probably ignore it, but I'd try to avoid it popping - not pedaling to full extension (straight leg) may help with that. If it's painful you may need to see a sports medicine physician or physical therapist to see about treatment options. Meniscectomy (removal of the torn meniscus) is the most common orthopedic surgery performed in the United States, but you don't seem to be complaining about pain so if it's just a popping you're probably okay. There are also other reasons why your knee might pop, but the meniscus is by far the most common. Hope it's okay.

Oh, and this doesn't have to be due to an acute injury. You can have a degenerative meniscus - it just wears out over time. How old are you? I'm approaching 40 and my right knee has begun to display some of the classic signs of this degeneration. Doesn't keep me off my bike. In fact, since I started biking to work a couple months ago my knee has been feeling significantly better.