The Atmel AVR Studio tools include an assembler and C compiler, and only run under Windows. A debugger and simulator are available. I'm using Studio 5 on a Win7 x64 laptop. Studio 5 is available here:
Operating systems aren't usually used with microcontrollers like the 8-bit AVR.
You typically write your code using the Studio text editor, in assembler or C, assemble or compile it in debug mode, and debug it on your hardware using something like an AVR Dragon, which is available from Atmel distributors. When it is working, you build the program for release mode, and program the chip. It will then run standalone.