General information on stream restoration:

EPA Restoration   Primarily focused on wetlands.

USDA Stream Restoration A wealth of general information

The Wildlife Society's Restoration Working Group   Encompasses all ecosystems, but contains good info on current scientific research.

The Center for Watershed Protection Many useful documents and publications for download and sale

Creekbank  A variety of information on stream restoration from an angler's perspective

Watershed Restoration Information Center  Currently still under development but hopes to be a clearinghouse for information

Alternative Stream Research A private project looking at the problems in stream restoration today.  Lots of photographs.  A good place to begin dialogue.
 

Some university programs with research on stream restoration:

University of California-Berkeley Department of Landscape Architecture and Environmental Planning

Colorado State University Department of Civil Engineering Stream Restoration Program

University of Georgia Institute of Ecology and River Basin Science and Policy Center

University of Idaho Department of Civil Engineering

University of Maryland Graduate Program in Behavior, Ecology, Evolution, and Systematics

University of Michigan School of Natural Resources and Environment

Monash University, Australia School of Biological Sciences

University of Montana Flathead Lake Biological Station

University of New Mexico (and University of Alabama) Freshwater Sciences Interdisciplinary Doctoral Program

North Carolina State University Stream Restoration Institute

University of Washington Center for Urban Water Resources Management and Center for Streamside Studies
 

Monitoring stream restoration projects:

Urban Stream Restoration Practices: An Initial Assessment (summary)
    A great analysis of urban projects in Maryland and Illinois available for purchase from the Center for Watershed Protection

Instream habitat structures in Klamath National Forest  The Klamath Resources Information System

Estimates of Production Benefits for Salmonid Fishes from Stream Restoration Initiatives  British Columbia Watershed Restoration Management Report

Impacts of riparian restoration in agricultural areas  National Environmentally Sound Production Agricultural Laboratory

Assessment of the Effects of Stream Enhancements on Flame Chub  Jeff M. Selby, Southern Division of the American Fisheries Society