The RF Telecommunications System for the New Horizons Mission to Pluto [pdf]
boulder.swri.edu
boulder.swri.edu
Other than the high end parts used in this device, it is fairly low-tech compared to most modern communications systems. That is a good thing for something like this I guess.
From the paper, even this amazing stability isn't good enough for their navigation needs, by itself:
7. NAVIGATION SUPPORT
The downlink frequency from the New Horizons transceiver is
derived from the USO, as discussed previously, but even this
excellent frequency reference is not sufficient to support
precise and accurate Doppler velocity measurements at the
target level of 0.1 mm/s throughout the mission. In order to
remove the impact of frequency drift and bias in the
reference oscillator, New Horizons has implemented the
noncoherent Doppler velocity measurement approach [2] which
was successfully demonstrated in 2002 during the demanding
Earth orbit phase of the CONTOUR mission [3].In addition, as another commenter noted, the reference oscillator is used for REX (the radiometry experiment on board New Horizons) and quality of gathered measurements for this experiment was one of the primary needs here: being able to use the component for the communications subsystem is just good power/mass engineering at work.