LEAP#173 Mini 64-LED Cube
Here's my "mini" 4x4x4 cube - 3cm per side with 3mm clear blue LEDs. Pretty compact, and delivers nice effects. The clear blue LEDs work really well - very bright, even when driven with minimal current.
It's encased in a Ferrero Rocher cube box. During the build, that raised some challenges - most of the effort in building the project concerned squeezing all the electronics into the space in the lid (which becomes the base of the cube). Not quite as small as HariFun's "World's Tiniest RGB LED Cube" but about as small as you can get without resorting to SMD LEDs!
As always, all notes, schematics and code are in the Little Arduino Projects repo on GitHub. Here's a quick demo: