I have also researched this, having previously done this type of upgrade on an E34 525i touring to 540i / 750i brakes.

3.0 (gas & diesel) and 4.4 have the same front & rear brakes. Front is a vented rotor (324 x 30 mm), rear is solid (324 x 12 mm).

4.6 & 4.8 have BIGGER front vented rotor (356 x 36 mm) to better dissipate the heat from the bigger caliper (also specific to 4.6 & 4.8 versions) with a larger diameter piston. 18" wheels are the minimum diameter required.

4.6 & 4.8 have a VENTED rear rotor (324 x 20 mm) to better dissipate the heat.

Master cylinders are the same for all engine sizes.

The only reason to do this for an 3.0 or 4.4 is if you do a LOT of high speed driving, VERY serious autocross or competition or pull some heavy trailers. Changing the rears to vented will not give you more STOP force but rather more mass to handle heat dissipation or better manage fade. Front will give you both more stopping ability and more heat fade absorption.

Consider Ate PowerDisc's, a good product that is TüV approved.