These are from a list that I copied and pasted a while ago. Accuracy is not guaranteed. Frequencies may or may not still be in use.
North Side:
160.32000 - North Side (North Station, Newburyport Line, Rockport Line, Haverhill Line)
160.52000 - North Side (while on Pan Am dispatched territory such as the Fitchburg and Lowell Lines)
160.59000 - North Side (Fitchburg and Lowell Lines in MBTA Territory)
160.69500 - Engineering (Track, Builing, Bridge, and Signal Maintainance)
161.56500 - Engineering (Track, Builing, Bridge, and Signal Maintainance)
160.87500 - Boston Engine Terminal
161.16000 - Pan Am Dispatcher (while on Pan Am dispatched territory such as the Fitchburg and Lowell Lines)
161.46000 - Mechanic Help Desk
South Side:
160.68000 - CSX NA Dispatch (Worcester Line)
160.80000 - CSX Road Channel (Worcester Line)
Dispatchers and Trains both use the same frequency for these:
160.92000 - South Station, Northeast Corridor Lines
161.49000 - Old Colony Lines
These may or may not still be in use:
470.66250 - MBTA Police Channel 1 - PL Tone 131.8
483.56250 - MBTA Police Channel 2