What exactly are you envisioning? Obviously you don't want to upload sketches via the arduino IDE, since it already performs a reset to enter the bootloader. You do want to upload sketches wirelessly or something?
If you do, let me know, i've done exactly that (Bluetooth).
Entering the bootloader using a watchdog timeout is easy, include the wdt.h file on the top of your sketch
#include <avr/wdt.h>
then you can use something like this to enter the bootloader on recieving a specific character.
if(Serial.available())
{
char = Serial.read();
if( char== '#' )
{
wdt_enable(WDTO_30MS);
while(1) {};
}
}