Sega Dreamcast, Nintendo Gamecube.Side note: Based on comments in the article, it seems the size of the logo is a maximum of 1mm w/h.
http://www.wired.com/gadgetlab/2011/04/gallery-silicon-art/?pid=1650
http://en.wikipedia.org/wiki/VMU#Technical_specifications
Gamecube, Famicom.
Source.
Luigi’s Mansion.
Donkey Kong 64.
Sonic Adventure 2.
Custom Robo.
Super Mario Sunshine.
Submitted by Eliser via Youtube.
Metroid and Geist.
Submitted by Josh Britt.
Paper Mario: The Thousand Year Door.
Submitted by Chrono_blazer.
The Legend of Zelda The Wind Waker.