I've got plenty of responses from people who found the Treasure Chest, and also heard from some people who have the good dope on regional rail trails.  

First, because it's short and sweet, I got a shout out from Carl Knoch of the Rails-to-Trails Conservancy. They have a website with information on rail trails all over the U.S.

Next up, a local biker, Paul Berkebile, writes of his experience on some local trails, and offered this nh.gov link for more information on NH rail trails and bike routes.

Paul also sent a map showing the state's major rail trails: nh_trails_1-1.pdf 

Paul writes:
I have ridden the Granite Town Rail Trail, it starts at the parking lot adjacent to the Milford Public Works garage on South Street (Route 13).  Although the official listing may say it is only two miles long the old rail bed can be ridden a lot further than that, probably all the way through Brookline to the Mass line.  The one time I rode it I took a left when the trail forked and soon found myself at the end of that branch, I'll try the right branch sometime.  This trail is not really maintained down that far and there are tree roots and even the old ties in one area.  A mountain bike is really called for but I negotiated it on my hybrid.

Where the trail crosses Union Street, just before going under route 101 you have to find your way around the west end of the guardrails and from there it detours around under 101 and across Armory Road, then goes over a small hill to avoid some development before it actually gets back on the railroad grade.

Just after a rain there is a low area in a cut in the rocks that fills with water, not deep but a nuisance.  That area is pretty far down, in Brookline I'm sure.

The Greenville-Mason trail is closed a little distance south of Pratt Pond because the spring rains this year washed out the bridge in the deep gully there.  It should be possible to find a detour around that section as it is paralleled by a road. (NOTE - It is possible, and pleasant, to detour past that section on local dirt roads - A.W.)

I met a couple from the Townsend area while riding the Bennington rail trail and they were part of a group that is working to get the trail extended into Mass.

I'm not sure about the paved trail from Jaffrey to Ringe, I have ridden an unpaved trail there that goes from Jaffrey to the state line.  It continues into Mass. but you quickly find yourself in an old induatrial area in Winchendon where the trail disappears and you have to get on roads.  If you know where to look you can find the beginning of the trail in Jaffrey but it is easier to continue south on 202 until you come to County Rd on the left.  The trail goes through a boat launching area at the end of County Road where you can park.

The other trail you mentioned that runs through Troy actually starts at the state line, there is a small parking area near the State Line store.  This also continues south into Winchendon but this one is really destroyed in Mass.  I've ridden it but parts of it are unrideable and you have to push the bike. In NH this trail runs from the state line to Route 101 in the eastern end of Keene (I think it is in Keene).  The maps show it contimuing into Keene but that is incorrect, the part north of 101 is grown up in brush in peoples back yards.
The last time I rode this trail (last year) the part of the trail between Bowker Pond, just south of Troy and the town of Troy was closed because of superfund cleanup site at the old Troy Mills.  It was necessary to take the road up the north side of the pond and find your way on roads into Troy and pick up the trail there.
A few notes on some of the other trails:
The Ashuelot branch south of Keene is in fair condition as far as I have ridden it but definitely mountain bike or hybrid territory.  Pick it up on the Keene State athletic field complex south of 101.  Norm's Bike Shop is there and the owners seem pleased to have bikers park there.  From the bike shop parking lot make a left on the service road, cross the pedestrian birdge and find your way to the other side of the athletic fields.  Immediately after going through the gates, before the speed bumps, make a left onto the trail.

You can get to the Cheshire branch from the same place but turn right at the gate.  You have to cross 101 but an opening in the traffic usually opens.  Once in Keene you follow the trail, which is mostly obvious, through town.  Crossing route 10 is a little challenge but after that you are on a trail that is decent as far as I have ridden it.  You could also get on the trail at one of the gates on the local roads west of route 10

The Bennington-Hillsborough trail is a nice ride, pick it up at the old train station in Bennington.  It just kind of disappears as it enters Hillsborough.
I am told that the Northern Railroad Western Section is a nice ride but I haven't been on it.  The Eastern Section, at least the beginning part north of Concord appears to be maintained by a snowmobile club that covered it with crushed granite, the problem is the gravel stones are about 1.5 inches across and a bike plows through them instead of rolling over them.  Impossible to ride.

The Rockingham rail trail can be ridden, I've done the full length on my hybrid.  Like you say parts of it are torn up by ATVs and difficult to ride.  I had Leg cramps after plowing through the entire trail both ways in one day.  There is some nice scenery though and it is worth riding at least part of it.  Get on at the parking lot at Lake Massabesic on Route 28 just south of the Candia traffic circle.