Are Common Mode Choke Coils needed on USB?
The USB signal is not entirely differential, so it's not a great idea.  (The end-of-packet (EOP) signal is both pins pulled low, which, I believe, is why there's always noise at 1 kHz and harmonics in USB systems, since it's sending common-mode signals every 1 ms.)


A common mode (CM) choke should be used to terminate the high speed USB
bus if they are need to pass EMI
testing. Place the CM choke as close
as possible to the connector pins. See
Section 5.1 for details.

Note: Common
mode chokes degrade signal quality,
thus they should only be used if EMI
is a known problem.
Common mode chokes distort full speed
and high-speed signal quality. The eye
diagram above shows full speed signal
quality distortion of the end of
packet, but still within the
specification. As the common mode
impedance increases, this distortion
will increase, so you should test the
effects of the common mode choke on
full speed and high-speed signal
quality.

High Speed USB Platform Design
Guidelines

Note:
additional filtering may be achieved by winding the 4 wires through the ferrite bead an additional turn. As
with the use of ferrite beads in signal paths, care should be taken to insure that the signaling meets rise
and fall times, especially the EOP signaling. EOP signaling is single ended and may be strongly affected
by a single bead, which acts as a common mode only filter.

Intel EMI Design Guidelines for USB Components