I am looking forward to a leaf peeping tour of New England in October. Being from a very small rural town, I would prefer to find lodging in small rural towns in NH, VT and ME.
I am interested in advice regarding rural town lodging along scenic leaf routes. Thanks.

I live in a small town, too, but I think New England has some great small cities where you can enjoy as a base for day trips. Portland ME has great restaurants. For VT, Burlington and Middlebury are nice but Brandon is smaller and might be what you are looking for. In NH, Concord has a great, walkable downtown with some pretty good restaurants, an independent theater and things going on in the evening. Warner is one of my favorite small towns but lacks a good choice in restaurants for dinner. Center Sandwich is one of the prettiest towns in NH and has a good restaurant (Corner House) but I don't think has any lodging.
What you need is a good map that shows alternate routes because there will be traffic congestion on the interstates. Don't rely on a map of New England. The one I use has NH and VT on one side, Maine on the other. You should be able to see that you can take Rt 103 from downtown Concord (starts out as Pleasant St) and head for New London without going on I89 which is parallels for several towns. You can take a slight detour to Gould Hill orchard (nice view from there and wonderful apples) and in Warner can take a detour up Mt Kearsarge.

If you have a good navigator or can plot out your own route, Delorme publishes a state atlas and gazetteer for each state. It's oversize but shows every road including seasonal ones, the location of things like waterfalls and covered bridges.

I would caution that the depopulation of some parts of rural New England means that gas can be hard to find, even along some of the interstates, notably 89. I would pay attention to my gas gauge as I left population centers.

In other places, the quietest village will have a twenty pump Irving Oil station that has as many lights as Cape Canaveral.

Look at Jackson NH

I was going to post the same town as wupa.

If you do go to Jackson, check out The Inn at Ellis River. I stayed there last year - late summer, not foliage season - and loved it.

There are many pleasant small towns in Northern New England that would be a good base for leaf peeping (I live in one).
Here are a few that are not too touristy that come to mind:
Vermont: Grafton - Grafton Inn, Rochester - Harvey's Mountain View, Norwich - Norwich Inn, Waitsfield - The Round Barn Inn
New Hampshire: Lyme - Loch Lyme Lodge, Sugar Hill - Sugar Hill Inn.
There are hundreds more.
Nearly every where you drive in Vermont and New Hampshire you will see amazing foliage. There are a few areas that are more 'urbanized' like the Manchester-Nasua-Salem area of New Hampshire, and just south of Burlington Vermont, but in general nearly all of both states are quite rural.
Yankee Magazine's website might be a good resource.

Check out Bethel Maine.

I used to love Tilton, NH...amazing foliage and a stop at Kellerhaus for incredibly yummy candies, chocolate, and ice cream sundaes! http://www.kellerhaus.com/icecreambuffet.htm

Also, here's a thorough guide on leaf peeping through the areas you mentined: http://www.yankeefoliage.com/drives/newhampshire/all

Note about above post, Kellerhaus is in Weirs Beach, NH not Tilton. There isn't anything to see in Tilton exempt the outlets at exit 20 (if that's of interest).

Most of New Hampshire is great in the fall. Another area that is very "New Englandy" and beautiful in the fall is in southwest NH - the Peterborough area in the Monadnock Region (route 101 is the main road to get there). http://www.visitnh.gov/welcome-to-nh...ck-region.aspx

The Lakes Region and Lake Winnepesaukee is going to be beautiful too. Take a fall foliage cruise on the Mount Washington boat. http://www.cruisenh.com/index.php

There are several small VT towns one can consider -- I've liked Middlebury and Woodstock, for two.

Yes, sorry. I wasn't saying Kellerhaus was in Tilton, but that we always stopped there after a day in Tilton.