  We determine characteristic timescales for the viscous damping of r-mode
oscillations in rapidly rotating compact stars that contain quark matter. We
present results for the color-flavor-locked (CFL) phase of dense quark matter,
in which the up, down and strange quarks are gapped, as well as the normal
(ungapped) quark phase. While the ungapped quark phase supports a temperature
window between 10^8 K and 5x10^9 K where the r-mode is damped even for rapid
rotation, the r-mode in a rapidly rotating pure CFL star is not damped in the
temperature range 10^10 K - 10^11 K. Rotating hybrid stars with quark matter
cores display an instability window whose width is determined by the amount of
quark matter present, and they can have large spin frequencies outside this
window. Except at high temperatures T > 10^10 K, the presence of a quark phase
allows for larger critical frequencies and smaller spin-periods compared to
rotating neutron stars. If low-mass X-ray binaries contain a large amount of
ungapped or CFL quark matter, then our estimates of the r-mode instability
suggest that there should be a population of rapidly rotating binaries at
frequencies greater than 1000 Hz which have not yet been observed.
