I use the AUX connector with my iPhone, which I place into the cupholder. Very convenient, does not get in the way of my hand/gear shifting, doesnt move and easy to pull, change song, and stick back in.
Also, see this thread for my pics on how I ran the AUX cable (you pretty much can't see any but an inch of two of it):
Ideas on how to best hide the 3.5mm AUX cable coming out of stock/base stereo?