The negative signs are more a thing of convention than anything...
I think what jtbell wrote is useful. Often, an object in a bound state, like an atom in a ground state, or a spherical planet, must be at a minimum of potential energy.
The easiest way to do this is to say that a potential energy of zero means the system is totally unbound (imagine an ionized atom), and obviously, the bound state would have to have a negative energy, -3GM
2/5R, for a planet, star, etc.
You can also think of the positive of this as being the energy required to unbind the system, so the energy needed to ionize an atom, or the energy required by the Death Star to disintegrate Aldreraan ;)
There is an arbirarity to potential energy. You can set the zero point energy to be anything as long as you are consistent. There are standard conventions for some systems like gravitational binding energy that make everything much nicer, however.
I'm guessing this is the wiki page you're referencing?
http://en.wikipedia.org/wiki/Gravitational_binding_energy
I see that they use the positive and negative version of the equation. It makes little difference. It only matters the convention. The top equation is essentially saying that this is the energy stored in the gravitational binding of the object, and the second equation is saying that this is the total binding potential of the spherical object , which is negative if we say that the potential zero point is when the system is completely unbound.