3D is flying in 3 axis, thats where the 3 comes from.
Taken from
www.3drc.info
The term 3D is arguably specific to RC Helicopters, but it has been adopted by fixed wing fliers too, and through publication, has become one of the RC World's everyday terms.
The normal motion of airplanes occurs in the 2D plane, or a imaginary plane that parallels the wings and extends to infinity. There is no "depth" to this 2D plane. All motion in normal 2-dimensional flight is restricted to that infinite plane. In other words, there is motion in 2 axis of the aircraft. Rolls, loops, knife edges, and hammerheads (among many others) constitute 2D flight.
3D flight is when the motion of the aircraft extends to all 3 axis, where the aircraft has a motion that moves out of the plane of flight. Examples of this are spins, hovering, blenders, rolling loops or circles, and lomcevaks, just to name a few."
Many thanks to Teryn DalBello for this definition.