I was thinking about this and figured it would be good for everyone to figure these things out. Coming up with a plan to make it easy to see turned out to be easier than actually enacting the plan, ha.
I wanted to use the panoramic feature on my phone's camera to make an image where you were looking at each game head on. Then I was going to add some reference lines at different heights to make it easy to see how tall these boxes were in comparison to each other. The last couple weeks we've been moving stuff around a lot and I have a ton of stuff packed up so I was only able to get boxed games for this small group. It still shows some helpful info.
[img width=700 height=276]https://c8.staticflickr.com/6/5754/30163102455_5dbb538e2e_c.jpg[/img]
If you click on the picture you should be able to view it full size on flickr. It is 4785x1889 pixels if you download it.
Edit: link:
https://flic.kr/p/MXpMuBSystems from left to right:
The 3 Odyssey^2 board games, you'll need 6 1/2" for those
3DO
Vectrex
Intellivison
Master System (Genesis is same size) with hang tab
2600
PC common small box
Gamecube (standard DVD sized)
VHS
NES
N64 on end
SNES on end
Special Edition Blue Ray
Genesis without hang tab
PS3
Blue Ray
Odyssey2
Brazil Odyssey^2
SNES on edge
N64 on edge
Game Boy Advance
Saturn (standard CD case size
DS
Note that SNES on end is 7" and INTV is 8" but it is hard to see the 1" difference in the picture.
Dimensions are not exact but are very close, if you only leave 5" for your SNES games it will be a tight fit.
Panorama does some weird things:
[img width=700 height=212]https://c2.staticflickr.com/6/5686/29867633880_7267d1f03a_o.png[/img]
https://flic.kr/p/MviqYQI know the original question was about odd box sizes but this is what I had at the moment. Figure it's a start anyways.