For the conservation of energy to work, the sum of the Kinetic energy "T" of a body pulled by gravity, and it's gravitational potential energy "U", must be a constant.
T+U=C
Kinetic energy is always positive, and will increase as the body falls faster and faster towards your source of gravity. To compensate, U is going to have to be zero. If it was positive, the total energy C would not be constant.
Sort of a fudge, but necessary if you want the conservation of energy to work. You get around it by making the gravitational force equal to minus the gradient of the potential energy. [tex]F=-\nabla U[/tex].
A negative U makes sense in some way, because your gravitational energy, though always negative, increases as you move away from the body, i.e. upwards. You expect gravitational potential to do this, increase, as you move up, so that you'll gain energy as you fall. If U was always positive, but decreasing, it would mean that potential energy would decrease as you moved away from the body. Also, if you tried to make it always positive but increasing, though the potential energy would approach a maximium, your effort would be confounded as you moved close to the body, i.e. as x->0.
The choice of negative potential energy is really the best of a bad bunch. Try graphing the equation, then graphing it's negative. Move both graphs up and down by constants to get a feel for why the canonical option really is the lesser of many evils.