as AudioGuru said, there are no equations. the depletion layer depth changes with voltage, a graph in the data sheet for transistors, varicap diodes and regular silicon diodes is what there is to work with. if you know the surface area of the B-C junction and know the depletion layer depth you can use the standard capacitance equations, but when you get a data sheet, these values are not listed, as they aren't important enough to be included. you could use the chart or measure it for yourself and calculate an equation for C vs V for a particular device. the actual junction capacitances can be different from device to device, even with the same part number.
even if you knew the surface area of the transistor and the depletion depth, it still would not guarantee that you know the actual surface area of the B-C junction itself, because the base regions mask is usually a shape other than rectangular. on some power transistors it is E or H shaped or a series of circular rings.