If not necessarily by priority, then by order in which they popped into my head. . .
Currently trailed lines, medium-term
1. Lexington Branch - MBTA rapid transit (Red Line). Landbanking for the Minuteman is on a court-ordered "restoration without objection" settlement, so in theory the state holds the leverage here. In theory...I'm sure there are tons of well-studied loopholes. But on legalities this is how landbanking agreements should be negotiated, and for damn sure the gold standard for successful interim trails. Relatively easy one to rail-with-trail because it would be subway almost to Arlington Heights, then low-density rest of the way. Steep cost a lot more a factor than overpowering NIMBY's.
2. Manchester Secondary (inactive Hop River Trail portion, Manchester-Willimantic) - CDOT commuter rail (Hartford-Willimantic, continuing service to New London), NECR/CSO and P&W (overhead-only) freight. Likely the only direct Hartford double stack route from Worcester, New London, Vermont for P&W and NECR/CSO.
3. Franklin Line (inactive Southern New England Trunkline Trail portion, Franklin-Blackstone/P&W) - MBTA commuter rail (Woonsocket via Blackstone), P&W/G&U/CSX freight (alt route to Boston). Very easy to rail-with-trail. Trail's unpaved anyway because the Blackstone River bridge is out and it's disconnected from the rest of the Air Line. Undoubtedly a BETTER trail if a replacement bridge had a pedestrian berth next to active rail and they then had good reason to pave it east of the disconnect.
4. Armory Branch, state line-Springfield - CNZR/CSO freight and Springfield Line freight bypass. Likely the only direct Springfield-south double stack route for CNZR/CSO interchanges with CSX/PAS (Springfield Line with too many clearance issues). If Springfield Line goes HSR, Amtrak may start agitating to get freight booted to secondary routes by jacking its already high freight overhead rates as leverage. Small trail in Longmeadow, driveway/courtyard encroachment in Springfield but no structure encroachment (gas main underneath). National pressure the only way to restore this one because MA's let the towns chew it up, but national interests re: the Springfield Line could overrule if reactivation need comes down to that.
5. Falmouth Branch - MBTA/CCCR passenger. Not soon, but long-term there's going to be some deep regret about ripping up those tracks when the rich folks can no longer get anywhere due to unbearable Route 28 traffic. Unfortunately it'll manifest itself as whining to give them their own Greenbush Line handout...but, bleh, no short-term memory/no long-term memory when it comes to NIMBY's and recovering NIMBY's.
6. Chicopee industrial track (the one they just ripped up) - PVRR freight. Yeah, too late now, but shame on them for nuking a line with customers interested in service right now.
Potentially/imminently trailed lines that need to be kept open or otherwise VERY TIGHTLY regulated
1. M&L, Methuen - MBTA commuter rail (Lawrence-Methuen/Rockingham Park). 99-year trail lease given last year to trail nonprofit pushing the Iron Horse Preservation scam. Only ROW that can divert traffic off I-93 at the border, trailed portion in NH is in state rail plan as future reactivation corridor...ceding usage control to 1 town + non-profit in MA shoots that down forever.
2. Millis Line, Needham-Medfield - MBTA commuter rail. Aggressive, very anti-rail trail lobby using dubious tactics to try to take the line.
3. Eastern Route, Newburyport-Portsmouth - MBTA/NHDOT commuter rail (Portsmouth). Small portion in downtown Newburyport trailed, but only constrains restoration to single-track without blocking. Sale of Hampton Branch to state of NH needs very forward-thinking interim planning to not block reactivation (good rail-with-trail corridor if they can provision it smart enough).
4. Fitchburg Secondary, Fitchburg (inactive portion past Leominster yard to Fitchburg Main) - MBTA commuter rail (Framingham-Clinton/Leominster), CSX-PAS freight interchange. Trail is off for time being because of town disputes with CSX. Probably worth cooling it for a bit, at least until the state can consolidate ownership of the whole line. Commuter rail proposed Framingham to Northborough/I-290 with future Leominster extension potential; Fitchburg Line connection highly desirable on any CR configuration for equipment moves. Slim chance of freight interchange reopening if Worcester Branch congestion makes alt route desirable (doubtful if CSX retains ownership; very remotely possible if state owns and sweetens CSX's pot). For such a small stretch of inactive ROW, the rest of the active line pretty secure long-term, and such a small/cheap gap to reconnect, I wouldn't allow anything to block this line. Don't even change the designation from railbanked to landbanked.
5. Plymouth Line, Plymouth Center - MBTA commuter rail. Originally planned terminus of restored Plymouth Line...NIMBY infighting stopped it at Cordage Park, but they'll likely have no short-term memory in 10 years when downtown traffic gets bad and start bitching about needing rail.
1 & 2 are the most senseless, damaging, clear-and-present danger trail proposals currently going. Methuen is a total "WTF were you thinking???", and if the T was dumb enough to gak that one away I have no confidence they'll be able to rebuff the equally flimsy Medfield one. Others listed are manageable provided the states can start applying the landbanking laws a fraction of the way originally intended without the NIMBY's having 99% of the power and game being over before it ever was suggested.
Long-term holds (interim trail OK if protection is vigilantly maintained and "toothy" enough to overpower opposition)
1. Central Mass, Route 128-Sudbury - MBTA commuter rail (new junction past 128...duplicate Waltham section not needed). Weston is blocking the trail on homeless deviant bicyclist grounds or something stupid so current trail from Hudson can't extend east of S. Sudbury/Bruce Freeman Trail. It's pretty much a dead issue for foreseeable future. Line may be needed to S. Sudbury for Route 20 congestion, so state needs to be very careful about Weston/Wayland NIMBY games. Current Hudson trail's nonprofit is amenable to rail-with-trail if future Hudston/West Berlin service desired beyond S. Sudbury.
2. M&L, Salem-Derry/Manchester - MBTA/NHDOT commuter rail. NH state-controlled trail currently. Key is preserving the Rockingham Park-Lawrence portion and keeping it away from the Methuen lobby looking to insert a locally controlled blocker. I can't overstate how stupid, senseless, and utterly short-sighted the T was to sign its life away for 99 years to a local-yokel Iron Horse scam on the only possible cross-state relief valve for I-93. I can almost hear all of NHDOT's traffic engineers screaming "Noooooooooooo!" in pain.
3a. Air Line (+ Manchester Secondary), Willimantic-Putnam - Amtrak 2040 inland NEC routing option.
3b. Air Line, Putnam-Blackstone - Amtrak 2040 inland NEC routing option if they want to skip Worcester for a Boston direct (I'm betting not...short jog north on P&W + B&A east can handle it on upgraded infrastructure much cheaper with little schedule penalty, and Worcester is way too big a city to skip).
4. NH Main, Boscawen-White River Jct. - Amtrak Boston-Montreal regional or HSR. Not a protection risk as it's an NH "as-is/no-warranty" unmaintained snowmobile trail, so state holds all the cards and only needs to keep it that way.
5. NYNE/Washington Secondary, Providence-Plainfield - Hartford-Providence intercity rail via Willimantic. Trailed in RI, landbanked w/no trail planned in CT. Probably won't support rail-with-trail on dense Warwick portion, but trail a good interim use to enforce encroachment protection.
6. Framingham Secondary (Taunton-Mansfield gap) - CSX/MassCoastal freight, accessory MBTA commuter rail bypass. If CSX double-stack to Middleboro needed for future deep-dredge South Coast ports, NEC all the way to Attleboro is not an option. Can get around the obliterated downtown Mansfield ROW by restoring to Mansfield Airport, snaking it on a new-construction re-route hugging 495/140 for 1.5 mi., then 0.5 mi. on NEC freight siding (passenger-separated) to Mansfield Jct. (no overhead bridges north of 140, cat supports can readjust wires to DS height without affecting Amtrak performance). Probably not needed for any reason but DS to Fall River/New Bedford, but needs to be kept open as ultra-long range contingency because port carloads not easily predictable at >30 year ranges when deep-dredging factored in.
7. Portsmouth Branch, Newfields-Manchester - PAR freight, (maybe) NHDOT commuter rail Concord/Manchester-Portsmouth. Don't know if there's any trail here currently. The only restorable connection linking the NH Main, Western Route, and Eastern Route on a single shot. May be needed to spread freight traffic between the Main and WR when passenger congestion on each increases. Only way to do in-state CR linking Concord/Manchester metro area with Portsmouth/Kittery metro, only way to transfer passenger equipment between all 3 NH passenger mains north of North Station. Freight may bump this to a medium-term need if the north-south passenger traffic really explodes.