For those, who want simply flash utility for Atmel's SAM family, here is a solution:
http://www.shumatech.com/web/products/bossa
It works fine with my sam3s4c.

If only it worked... Doesn't seem to recognize AT91SAM9261S rev B. I see it's CDC driver has installed itself, but no luck. Maybe it's just missing the chip ID?

By the way, downloading doesn't work with SAM-BA either (due to running win 7 64-bit). I either have to suffer with less ram for my development machine or have a second machine just for downloading firmware.