Stripped down Arduino
1. Upload the ArduinoISP sketch (in Examples/ArduinoISP) as per usual to the Arduino board via the USB or serial.
2. Change Arduino to manual as opposed to auto-reset (I have used a seeeduino with a little switch to allow this).
3a. Log out of the IDE
3b. In (Windows) C:\Documents and Settings\username\Application Data\Arduino\preferences.txt change the line
upload.using = bootloader
upload.using = arduinoisp
4. Wire the proper Arduino --> stripped_down_arduino
5V --> 5V
GND --> GND
D10 --> RESET
D11 --> D11
D12 --> D12
D13 --> D13
5. Open the Arduino IDE application and change the Tools/Board to match the stripped_down_arduino (if this is different from the proper Arduino that will now be acting as ISP)
6. If this is the first time that the processor on the stripped_down_arduino has been programmed you will need to upload the bootloader (Tools/Burn Bootloader/w. Arduino as ISP) otherwise it will not use the crystal for the clock. Otherwise just upload the sketch to the stripped_down_arduino