Transmutation of nuclear waste usually refers to the burning or transmutation of transuranic (TRU) waste in a subcritical nuclear reactor, driven by a proton-accelerator-driven neutron source. This is often referred to as ATW (or Accelerator for Transmutation of Waste). See
http://www.wipp.energy.gov/science/adtf/ATW.pdf
This article is a summary of a thorough study of the major required technology developments, the timescale, and the cost of an ATW. One concern might be that the U.S. would probably only [STRIKE]one[/STRIKE] eight of these (life cycle cost $279 B, see page 7-3), so it means shipping all the TRU waste to [STRIKE]a[/STRIKE] [STRIKE]single[/STRIKE] few sites for processing.
Like reactors, the thermal energy (and electricity) output of the ATW is larger than the energy input, like for running the proton accelerator. Furthermore, because the ATW reactor itself is subcritical and can only become critical when the accelerator is on, there is no startup criticality problem with reactor "poisons" like xenon-135. See
http://en.wikipedia.org/wiki/Neutron_poison
Bob S