I have been using and programming for avr microcontrollers from years, initially as a newbie(which is still consider myself) i used WinAVR and still use it for small and easy programs, but the problem with WinAVR is that its been years nobody bothers to update the environment although you can use the updated avr-gcc tools by downloading and replacing it in existing installation which is little complicated and i find it difficult to set things up and then explain it to others, so just leave the WinAVR as it is. Hey lets call it VintageAVR from now on. Talking about Atmel Studio well i think this is the coolest software one must use but again it is huge and might become pain for low configuration machine plus not available on mac and linux machines, why are we even talking about this? well just to give the background if you are just about to start with AVR microcontrollers.
The reason i choose eclipse over the other two most popular softwares because of its awesome features, well stay tunned and you will find it out your self. Well you must also be aware of Eclipse arduino plugin too, Don't worry if you are not i well walk you through of that setup too, so that we can have core AVR programming and Arduino programming on one single environment awesome right. so lets see how its done.