Hello World on an AVR Micro Controller
therandombit.blogspot.com
therandombit.blogspot.com
http://www.avrfreaks.net/index.php?name=PNphpBB2&file=vi...
Effectively you upload the program to the Arduino using avrdude, then you can send signals via USB from your PC using the *nix program to switch the LED on & off. The final programs weren't posted, but you can piece them together from the comments :)
It was heaps of fun. If you have an Arduino but haven't made the leap, I highly recommend getting down and dirty with more typical AVR stuff.