Here is a detailed and well-illustrated overview of using Eclipse IDE as an AVR development platform by Sulaiman Salim Marhoun Al Habsi:
Using eclipse AVR application development plug in. at sulimanhabsi blog.
It is a second post about Eclipse on his blog and it shows a different approach to how many, if not most, DIY electronics and robotics hobbyists come to program Atmel chips – start with ATmega168 or ATmega328 in the form of an Arduino board and use Arduino IDE and Wiring version of C programming language as a starting point. Arduino IDE can be adapted for using it with other Atmel chips, such as ATMega8 which Sulaiman used as an example, and many if not most other Atmel MCU. The only ones missing Arduino IDE support (to the best of my knowledge) are the smallest of the AVRs – ATtiny12 , ATtiny10, 9, 5 and ATtiny4. I am wondering if Eclipse plugin for AVR is better it terms of the chips supported.
Anyway, if you program other things in C (or Java or whatever else for that matter that also has an Eclipse plugin) and have a need to program AVR chips, you may want to check out his blog for some useful pointers on setting Eclipse up for AVR and then using it to program the chips.