The Arduino IDE can be configured to program a variety of AVR microcontrollers, not just the Atmega328. However, while this capability is possible for many other chips, not all have been documented. This page contains links for configuring the Arduino IDE to program other microcontrollers, namely the ATtiny series.
Additional information on how to make your own modifications to the Arduino IDE for custom hardware
Customizing the Arduino IDE - A description of how to customize the IDE for your board