The radius R of the pulley has a fixed value of 0.500 m. This is quite a large radius. However, if the radius were much smaller, the inertial effects of the pulley would be very slight, as long as we take the pulley mass to be of the same order of magnitude as the masses of the blocks.
You should imagine the potential energy bar to reach up from negative infinity to its visible height, i.e., to extend below the bottom of the applet window. When the top of the potential energy bar is below its zero level at h = 0, the potential energy is negative. Potential energies can be negative, as can the total mechanical energy. Kinetic energies, of course, are never negative, by definition.
Note. The energies displayed by the applet belong to a system consisting of the two blocks, the pulley, the string, and the earth. PE2 is the potential energy of the pair consisting of Block 2 and the earth. For brevity, it is customary to refer to this potential energy as the "potential energy of Block 2."