There was Rb-based Ultra Stable Oscillator in outer space, delivered to Titan (VI moon of Saturn) inside the Huygens, brought there by Cassini. (DWE RUSO in http://nssdc.gsfc.nasa.gov/image/spacecraft/huygens_cutaway.jpg). Schemes and paper - RUBIDIUM ULTRA-STABLE OSCILLATORS AT TITAN: THE HUYGENS DOPPLER WIND EXPERIMENT, 1997. THE HUYGENS DOPPLER WIND EXPERIMENT. Titan Winds Derived from Probe Radio Frequency Measurements, 2002
There were some stable non-atomic clocks on several other probes. The Cassini itself was listed to have on-board Ultra Stable Oscillator (quartz-based, for navigation with Doppler effect), similar were used on some Mars missions: https://solarsystem.nasa.gov/docs/Asmar.pdf "ULTRA-STABLE OSCILLATORS FOR PLANETARY ENTRY PROBES", S.W. Asmar et al. NASA JPL (possibly from 2004)
Oscillators on NASA Deep Space Missions
The Voyager 2 USO is still working and the Voyager 1 USO ceased operations nearly 20 years after its procurement, exceeding specifications. ...
USO serial #4 was later flown on the Galileo spacecraft. ...
several deep space missions have carried USOs for Radio Science experiments (e.g. Mars Global Surveyor, Cassini). These oscillators were single-oven, SC-cut crystals with a typical Allan deviation of 1x10-13 at τ = 100 s. More recently, a flight-qualified USO is being prepared for proximity communications and navigation on the upcoming Mars Reconnaissance Orbiter mission
- The Huygens Ultra-Stable Oscillator
The ESA Huygens probe to Titan, carried by the Cassini spacecraft, has a Doppler Wind Experiment (DWE), a Radio Science experiment with requirements that were met with a rubidium (Rb) atomic standard 5.
Check also table from the paper - "Table 1: Representative data of parameters characterizing ultra-stable oscillators on deep space missions collected from various sources, in some cases published specifications and, in some cases, in flight data."
I found presentations about the topic and future experiments:
The best overview about USOs is again from Sami Asmar, from 2012: