Pyro,
You made me think (ouch that hurts). What if I used one arduino mega and remove its reset mechanism and instead hook it to an interrupt. Then it should be able to detect when the PC wants to reset it and receives serial transmission and pass it on to another port and flip the reset on the target board. This requires some special connector on the target arduino's shield for easy connection.
But I still don't know all the story about bootloader and programming. I am guessing the target arduino, if directly connected to a PC, also replies back to PC. Is there anything more sophisticated than just passing its reply through my programming arduino back to PC?