I typed these up for someone and thought I may as well post them :-)  I'll send a copy to wiretap as well.  

Atari System-1 Motherboard Pinouts taken from the Schematics.

Typed by:  Michael Stormoen  (mike@2084.com)

 P108
 ------
 1 Vid Rtn
 2 Blue
 3 Green
 4 Red
 5 V Sync
 6 key
 7 Comp Sync
 8 H Sync
 
 P104
 ------
 1  +5
 2  Coin Counter
 3  Coin Counter 2
 4  Unused
 5  Self Test
 6  Aux Coin Switch
 7  Unused
 8  Key
 9  Left Coin SW
 10 Right Coin SW
 11 Gnd
 
 P105
 ------
 1 Self Test
 2 Right Rtn (ground for audio)
 3 Right Audio (to amp section on AR/III board)
 4 Left Rtn (ground for audio)
 5 Key
 6 Left Audio  (to amp section on AR/III board)
 
 P101
 ------
 1  RTN (ground)
 2  + sense
 3  +5
 4  +10.3 V Reset
 5  - sense
 6  -15
 7  unused
 8  RTN (ground)
 9  +15
 10 +5
 11 +5
 12 RTN (ground0
 
Control panel wiring varies from game to game...
Here's what's on the schematics:
 
 J106
 ------
 1  +5
 2  n/c
 3  LED 2
 4  LED 1
 5  Key
 6  SW 5
 7  SW 2
 8  SW 4
 9  SW 1
 10 SW 3
 11 GND
 
 J102
 ------
 1  +5
 2  Up 2 / Vert. 4
 3  Dn 2 / Horz. 4
 4  Lt 2 / Vert. 3
 5  Rt 1 / Horz. 1
 6  Rt 2 / Horz. 3
 7  Lt 1 / Vert. 1
 8  Up 1 / Vert. 2
 9  DN 1 / Horz. 2
 10 Key
 11 GND
 
 J103
 ------
 1  +5
 2  Horz Clk 2
 3  Horz Dir 2
 4  Vert Clk 2
 5  Vert Dir 2
 6  Horz Clk 1
 7  Horz Dir 1
 8  Vert Clk 1
 9  Key
 10 Vert Dir 1
 11 GND
 
 Michael.
 www.2084.com
 mike@2084.com