New England Wilderness Act of 2006 - Title I: New Hampshire - Designates specified federal lands managed by the United States Forest Service in the White Mountain National Forest area of New Hampshire as wilderness areas and as components of the National Wilderness Preservation System (lands to be known as the Wild River Wilderness and lands to be incorporated in the Sandwich Range Wilderness).
Title II: Vermont - Subtitle A: Designation of Wilderness Areas - Designates specified federal lands managed by the Forest Service in Vermont as wilderness areas and National Wilderness Preservation System components (lands to be known as the Glastenbury Wilderness, the Joseph Battell Wilderness, the Breadloaf Wilderness, the Lye Brook Wilderness, the Peru Peak Wilderness, and the Big Branch Wilderness). Requires the Forest Service to allow the continuance of the Appalachian National Scenic Trail, the Long Trail, the Catamount Trail, and the marking and maintenance of associated trails and trail structures consistent with the management direction established under the Green Mountain National Forest Land and Resource Management Plan.
Subtitle B: Moosalamoo National Recreation Area - Designates specified federal lands managed by the Forest Service in Vermont as the Moosalamoo National Recreation Area. Directs the Secretary of Agriculture, acting through the Chief of the Forest Service, to administer the Area in accordance with laws applicable to National Forest System units and the management direction established for the Moosalamoo Recreation and Education Management Area under such Management Plan.