We’ve just posted a tutorial on upgrading the firmware on the ATmega8U2 on the Arduino Uno and Mega 2560. This should resolve the problems that some of you have had with serial communication between those boards and Linux. The upgrade doesn’t require a programmer or other hardware, just adding a resistor to the board and touching a couple of pins together. It’s a safe process, and if it doesn’t work the first time you can do it again.
We’re in the process of testing the new firmwares on other operating systems so that we can begin to ship them as the default on new boards. So far, though, many Linux users have had success with the upgraded firmwares.
Thanks to Dean Camera (author of LUFA) for his help in fixing the firmware.