Arlington Police has had a K9 for a couple of years now. Somerville wants to get one this year (and the money is apparently in the FY09 budget). I think that Medford had a K9 - dont know if they still have it. MBTA, BPD, MSP, and Hanscom AFB have PD dogs. Probably TSA, DOHS, FBI also.
The Arlington K9 went mutual aid to Cambridge and Lexington recently - so I dont think those agencies have dogs.