See particularly for commandline use:
http://www.arduino.cc/playground/Learning/
AVR programmer USB, stk500 V2 compatible
http://shop.tuxgraphics.org/electronic/microcontroller.html?id=2b93dd
http://www.tuxgraphics.org/electronics/200510/article05101.shtml
gcc-avr
avr-libc
avrdude
How streams of water can be used to create analogues of logic circuits
Scientific American August 1962: