I will do my best to explain it:
COM0: This uses a proprietary protocol to communicate between the control panel and the radio body. It is
extended over the internet by the RRC's, but can not otherwise be used for anything (for all rigs except Icom)
COM1 & 2: These are extended over the internet using a true serial server. COM2 is generally used to carry the CAT
signal between the rig and remote location, except in the case of a Twin configuration, i.e. K3, Yaesu, etc. In this
case, COM2 is used to tie the two locations together and you must use use COM1 for CAT if needed (mode-6 or 7).
If you are not using either COM port otherwise, then you can use it for serial control for rotors, etc.
COM3: This is used for special use of either FSK signal generation or Winkeyer emulation, user switchable (also
on the fly).
I hope this helps.
73,
Mitch DJ0QN / K7DX