I’ve been using a binder clip as a pen holder for about 6 months now. I use a soft cover pocket moleskine as a combination GTD / Hipster PDA / wallet (I call them iHips), and I use a 1 1/4” binder clip with a Pilot G2 mini along the top edge (as opposed to the side). The Pilot mini is a perfect fit, and with the pen clip over the back of the binder clip, the two are pretty much inseparable.
I find that mounting the pen on the top edge helps to keep it attached to the notebook in my pocket. Clipping the pen to the side makes it easier to dislodge, and also introduces a greater chance of damaging or breaking the pen. Obviously that’s less of a concern if you’re carrying your notebook in a bag, but this is essentially my wallet, so I mostly just slip it into a pocket and go.
One benefit the Pilot mini / binder clip combo has over using a full size pen is that you can write comfortably without ever removing the pen from the binder clip. You just fold the metal handles of the binder clip back into their normal positions once you remove the pen and clip from the notebook.