The Kopa rides very low in the pocket, and has a definite higher level of class than the plastic Calypso Jr (but costs more).
William Henrys ride very low, as does the Chris Reeve Mnandi (with a very discreet pen-like appearance), but we're talking a much higher price level here.
Some of the lowest-riding clips are the deep carry clips offered by knifekits.com (and Darrel Ralph's custom and middtech folders). These fold the clip over completely, so that there's none of the butt of the knife sticking out. All you see is the clip. But of course, if you're not buying a new knife, or making a kit, an existing knife might require modification.