Easiest and cheapest way to get digital outputs from a computer to the real world
Sounds like you intend to flash some christmas lights. :-)

Anything wrong with using an arduino or similar?
It would be fairly easy to expand the number of IO ports if the number of ports say on the mega 1280/2560 aren't enough. You can drive it via serial/USB terminal. You could use shift registers on the output pins of the arduino or you could use the i2c port expander and drive through that.

Using standard components like that will give you the shortest amount of prototyping time.

Note, my way may not be the cheapest. But it's effective and will actually get you rolling quickly.