Their last map concludes with the Allagash River - the classic (long before the NFCT) 50+-mile stretch from Churchill Dam to the St. John. If you're looking at doing a lot of paddling in Maine, there would be a strong argument for saving this, as a culmination. If you have three days and aren't sure you'll be Down East again any time soon, I think this would be your best choice. The NFCT map is the best I've seen, showing all the current campsites (as of May 2006).
The Mattawamkeag, not on the NFCT grid, is a very interesting three-day paddle, starting not too far south of Houlton (near the border with Nova Scotia). If ends with some fairly hairy (at least if you're in a loaded camping canoe) whitewater, in M'keag Wilderness Park, a little before where the M'keag joins the Penobscot.