I saw that a new Uno firmware had been uploaded to the Arduino repository. I've been trying it out, it seems pretty good so far, tools menu and serial monitor are much more reliable and it only failed to program once. (Although the Duemilanove was never perfect either)
I got the firmware from here:
https://github.com/arduino/Arduino/tree/master/hardware/arduino/firmwares/arduino-usbserial/(click on the right firmware, then click raw, then save it)
Reflashing the firmware on the 8u2 is a little tricky. Don't try this unless you are prepared to risk bricking your board completely!
You need the dfu-programmer utility:
sudo apt-get install dfu-programmer
Then follow the instructions here to get the Uno into DFU mode:
http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1285962838/10#10
Then to flash the firmware, do this:
sudo dfu-programmer at90usb82 erase
sudo dfu-programmer at90usb82 flash --debug 1 Arduino-usbserial-uno.hex
sudo dfu-programmer at90usb82 reset
Finally unplug the USB plug, wait a few seconds, plug back in.