Favorite topic here as I grew up near the branch in Concord, near the infamous "Filter Beds". My Dad recalls seeing a maroon and gold B&M switcher towing a box car, probably from Concord Lumber, shortly before the abandonment, and I spent many a day walking the right of way near the filter beds after the rails had been removed and the ties were left to rot. There were a lot date nails in them, mostly from the 20's. After awhile the town of Concord appropriated the ROW adjacent to the filter beds for sewage disposal; this was in a shallow cut just west of the grade crossing there, and the Great Meadows National Wildlife Refuge took over the portion next to it for their walking trail. That part is the best preserved and easiest to walk. There are precious few relics left; a tie here and there, and two ring posts, one east of the filter bed crossing, the other just west of Monument Street, surrounded by a tree!
I've hiked the portion west of the river around back of Nashawtuc Hill to Assabet Ave, back in the early 70's, and the rest of the way to Bedford as well, the last time being in 1974 when the Budd car was kept there over the weekends. Today I still get a chance to hike it from the Concord Wastewater Treatment plant to Monument Street (the cut has been restored to nature but overgrown, an adjacent path serves to maintain the trail), and it's used by bikers and walkers, even though there is a perpetual muddy spot in the cut just east of Monument Street.
The site of Middlesex Jct, where the branch reached is furthest extent connecting with the Old Colony Div. of the New Haven is almost impossible to find due to the fact that the prison farm has obliterated any traces of the right of way west of the rotary. However if you look at Google Earth you might be able to make out where the right of way used to be.
Reportedly the parking lot of the Concord State Police barracks is the site of the turntable at Reformatory Station. The B&M didn't go into the prison itself, it was a New Haven spur that served it from the yard at West Concord.
When I hike the ROW, I sometimes imagine all the 1900 era prisoners, no doubt in prison stripes and chains riding the rails to the "big house".