There doesn't seem to be a compiled list of console motherboard dimensions anywhere, so I figured it would be a good idea to make one. Here are pictures and measurements of most of the consoles I have. Note that the "unmodified" measurements usually include controller ports and such. The cut-down dimensions are estimates I've made based on grounding strips and blank sections on the boards as I have not actually done any cutting on any of these except an original NES board, so they may not be exactly correct. Some of the later consoles may have more than two layers in the board, so I'm not sure how safe it is to cut them. Also, I realize that some of the pictures are a bit blurry, so I may take better ones at a later date.
Atari 2600 (original): Size (unmodified): 9.75” by 5.375”
Size (minor cutting/relocation): 4” by 4”
Minimum size (major cutting/relocation): 3.75” by 2.75”
Minimum thickness: .4375” (note: My system has the three main chips plugged into sockets on the board. Some have the chips soldered directly to the board and are thinner)
Pictures:
Atari 2600 Jr.: Size (unmodified): 9.75” by 5.25”
Size (minor cutting/relocation): 8.75” by 4.75”
Minimum thickness: .3125”
Pictures:
Atari 5200 (2 port):Size (unmodified): 14.25” by 9”
Size (minor cutting/relocation): 14” by 8” (I’m not sure, but it looks like you might be able to cut off some of the sections all around the grounding strips because there aren’t that many connections going between them and the part inside the grounding strips. That would make the board 11.5” by 6.75”)
Minimum thickness: .4375” (As with the 2600, my system has the chips plugged into sockets on the board. I’m not sure if every 5200 is like that, so it might be possible to make it thinner.)
Pictures:
INTV System III (Intellivision): Size (unmodified): 8.5” by 6.5”
I didn't fully disassemble this one because the RF shielding was soldered right to the motherboard. I may desolder it for better measurements and pictures later.
Sega Master System 1: Size (unmodified): 11” by 6”
Size (minor cutting/relocation): 10.25” by 5.25”
Minimum thickness: .375”
Pictures:
Sega Genesis 1: Size (unmodified): 9.5” by 7.5”
Size (minor cutting/relocation): 8.75” by 6.75”
Minimum thickness: .375”
Pictures:
Sega Genesis 2: Size (unmodified): 7.5” by 7.5”
Size (minor cutting/relocation): 7” by 6.75”
Minimum thickness: .375”
Pictures:
Sega 32X:Size (unmodified):
-larger board: 7.5” by 3.25”
-smaller board: 2.75” by 3.875”
Size (minor cutting/relocation):
-larger board: 7” by 3”
-smaller board: 2.375” by 3.5”
Minimum thickness: .375” (you’d have to relocate a LOT of components to make it that thin, though)
Pictures:
Sega Saturn (model 1): Size (unmodified):
-main (large) board: 9.5” by 8.5”
-small board: 4.5” by 2.5”
-CD drive and board: 5.25” by 4.5” by 1.875”
Size (minor cutting/relocation): 9.25” by 8”
Minimum thickness: .5”
Pictures:

Sega Dreamcast (manufactured in 2000): Size (unmodified):
-main board: 6.5” by 5.625”
-CD drive board: 5.125” by 3”
CD drive: 4.5” by 3.5” by 1.25”
Size (minor cutting/relocation):
-main board: 6” by 5.25”
-CD drive board: 5” by 2.875”
Minimum thickness: .375” without heatsink
Pictures:

NES (original): Size (unmodified): 9” by 6.5” (7.75” by 4.75” with RF box removed)
Size (minor cutting/relocation): 7.25” by 4”
Minimum thickness: .3125”
Pictures:
NES 2: Size (unmodified): 6.5” by 4.25”
Size (minor cutting/relocation): 5.75” by 3.5”
Minimum thickness: .3125”
Pictures:
SNES (original) (smaller motherboard version): Size (unmodified): 6.5” by 6.25”
Size (minor cutting/relocation): 6.25” by 5.5”
Minimum thickness: .375”
Pictures:
SNES Mini: Size (unmodified): 6.5” by 4.25”
Size (minor cutting/relocation): 6” by 3.75”
Minimum thickness: .375”
Pictures:
Nintendo 64: Size (unmodified): 6.25” by 5”
Size (minor cutting/relocation): 5.75” by 4.75”
Minimum thickness: .375” (though heatsinks are necessary and will make it thicker)
Pictures:
Nintendo GameCube (later version with no separate power regulator board): Size (unmodified):
-main board: 6.25” by 4.75”
-CD drive board: 3.625” by 3.375”
-CD drive: 4.5” by 4” by 1.5”
Size (minor cutting/relocation):
-main board: 4.75” by 4.5”
-CD drive board: 3.25” by 3.125”
Minimum thickness: .375” without heatsink
Pictures:

PlayStation (original) (SCPH-5501): Size (unmodified):
-board: 7.5” by 5.5”
- CD drive: 4” by 3.125” by .75”
Size (minor cutting/relocation): 7.325” by 5.25”
Minimum thickness: .3125”
Pictures:


I'll add more consoles when I have time to take them apart. If anyone else would like to post pictures and measurements (even different revisions of the same consoles), feel free to do so.