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