Q: Can I use an Arduino board without the Arduino software?
    A: Sure. It's just an AVR development board, you can use straight AVR C or
       C++ (with avr-gcc and avrdude or AVR Studio) to program it.

    From: http://arduino.cc/en/Main/FAQ

As a side note, if you are feeling fancy, you can build your own firmware based on LUFA and load them into the Atmega chip the boards have as an USB-to-serial converter. That opens a world for pretty cool hacks too.