One of the simplest ways to calculate capacitance using PDE Toolbox is from the energy: C = 2*U/V^2 where U is the electrostatic energy and V is the potential across the electrodes.
The electrostatic energy can be calculated with this simple function
[dudx,dudy] = pdegrad(p,t,u);
energy = permittivity*sum(area.*(dudx.*dudx + dudy.*dudy))/2;
Since you are solving in the pdetool GUI, you will need to export the mesh and the solution to the MATLAB workspace before you can call this function and calculate the capacitance.
Another suggestion you might want to consider is turning on Adaptive mode on the Solver/Parameters dialog box. This option will refine the mesh (e.g. around sharp corners) to obtain a more accurate solution.