Good intro to use of extra pins on the newer/bigger Arduino Mega :

I just finished a quick sample project for the Arduino Mega, doing a project that comes up all the time, and usually requires a multiplexer, Max7219, or shift register: controlling 128 LEDs with a Mega. In this example, there’s nothing but a mega and 2 8×8 LED matrices. Whee!

And yes, that’s a nifty light blue prototyping shield designed by tinker.it and made by Smart Projects. Looking forward to using more of them.

[From Mega Knight Rider Example]