Are you restricted to Atmel's microcontrollers? If not, there are a lot of microcontrollers that can be programmed by simple hardwares, and appropriate softwares. For example, I can program most of my PICs (Microchip's microcontrollers) with a JDM-compatible programmer, and softwares like WinPIC (from DL4YHF), WinPic800, or PICPgm (I've got about 80 different PICs).
Are you restricted to Atmel's microcontrollers? If not, there are a lot of microcontrollers that can be programmed by simple hardwares, and appropriate softwares. For example, I can program most of my PICs (Microchip's microcontrollers) with a JDM-compatible programmer, and softwares like WinPIC (from DL4YHF), WinPic800, or PICPgm (I've got about 80 different PICs).