Unfortunately, there is a variety of problems surrounding the USB ports on the Raspberry Pi.
First there are power related problems, especially on the Model-B-V1 boards. The build-in fuses seem to cause problems with some USB periherals (http://elinux.org/RPi_Hardware#Power_Supply_Problems).
Even after all the improvements that happened in the firmware over last months, there are still problems with various devices and their drivers.
I had problems with a FTDI USB-2-serial converter used for the svxlink TRX interface. It would lock up the raspberry after a few hours 😦 Similar converters based on other chips (using other drivers) appear to be more well behaved.
I will have to add a dedicated post for USB audio, but a similar situation exists with such devices. Many provide choppy audio.
For all above problems there seems to be solution, even though with some limitations…
The USB port speed can be restricted to USB1.1 speeds by adding a kernel command line option. To do this, edit /boot/cmdline.txt and add the following option INTO THE SAME LINE as all the existing options you will find there:
The downside seems to be with USB keyboards. If connected they seem to lock up. This was no issue for me, as I only connect to the system over the network… talking of which – the Ethernet network will also be limited by this change. The 12 Mpbs still provide enough bandwidth for full-duplex audio and an echolink connection 😉