On another (randomish) forum, someone was flaming about errors in the published Uno R3 Reference Design , but they don't seem to have reported them on any of the actual Arduino-related forums. So I will...
In the R3 Schematic (both the EAGLE .SCH file and the pdf version), the USB power signal coming off of the fuse is mislabled (un-labled) n$2, when it should be "USBVCC":
And in the .BRD file for the PCB, there is a missing trace connecting the overvoltage protection circuitry on one of the USB signals to the USB Shield:
Interestingly, if you were to have a board made based on these files, it should still work. The misnamed signal has a PCB trace connecting it to the correct places, and the missing trace is in "protection" circuitry that shouldn't normally be relevant (and was not present prior to Uno.)