I'm going to show you how to make a 4x4x4 led cube controlled by an arduino duemilanove.
64 LEDS (color doesn't matter)
100 ohm resistors (you need 16 of them)
soldering iron and solder
Step 1: Making a Template
Get a piece of scrap wood and drill 16 evenly spaced holes into it. The spacing depends on the length of your LED leads. Drill the holes big enough to fit the LED into it. I used a piece of pegboard.