General - mouse
Bolon B. Internet resources for phenotyping engineered rodents. ILAR J 47:163-171, 2006
A very good source of links to Internet resources, not just about mutant mouse phenotyping, but also anatomy, histology, physiology, embryology, genetics, genotyping, and pathology.

Mouse anatomy
Cook's Anatomy of the Laboratory Mouse
Online at The Jackson Laboratory

Mouse necropsy
The Virtual Mouse Necropsy
Mouse Phenotyping 101: Necropsy and Tissue Trimming

Histology
Atlas of Laboratory Mouse Histology
Deltabase® Histology Atlas
Beresford Histology online
Roy Ellis's Histology Page - updated link?
Histonet
Search Histonet archives
Histosearch
Stains File
University of Bristol protocols
University of Utah manuals

Cryosectioning
Cryotechniques for Light Microscopy © Woods and Ellis 2000
Leica Tips for Cryosectioning

Immunohistochemistry
PHL Murine Immunohistochemistry Database (NCI-Frederick)
Rodent Immunohistochemistry (NIAID)
Laboratory of Experimental Pathology IHC Support (NIEHS)
IHC World - Changed
IHC Bookstore - changed
Immunoportal
IHC Resource Group - changed
Histochem.net

Mouse pathology
Center for Genomic Pathology
Pathology and Biology of Genetically-Engineered Mice - NIAID
Mouse Histology Protocol - The Jackson Laboratory Mouse Mutant Resource
Mouse Tumor Biology (MTB) Database Pathology Image Search - The Jackson Laboratory
NCI Mouse Models of Human Cancers Consortium Image Archive - University of California Davis
Pathbase: European Mouse Pathology Database

Mutant mouse phenotyping
Phenotyping of Genetically Engineered Mice ILAR J 47(2) 2006
Phenotyping Services - The Jackson Laboratory 
Johns Hopkins University Phenotyping Core
Mouse Phenotyping Service - Yale University
Phenotyping Services - University of California Davis
Mouse Phenotyping - Ohio State University College of Veterinary Medicine
Mutant Mouse Pathology Laboratory - UC Davis - changed link
Phenotyping labs - MyMouse.org

Diseases of laboratory animals
Common Infectious Diseases in Laboratory Rats and Mice
Charles B. Clifford, DVM, PhD (Charles River Laboratories)
Diseases of Research Animals - UMO RADIL
Opportunistic Infections in Laboratory Rats and Mice ILAR J 39(4) 1998
Emerging Diseases of Laboratory Rodents - Taconic
Helicobacters - Taconic
Murine norovirus - Taconic

UAB facilities
Center for Metabolic Bone Disease Histomorphometry and Molecular Analyses Core
Comprehensive Cancer Center Tissue Procurement Shared Facility
Molecular Pathology and Human Cell/Tissue CoreNeuroscience Core - Molecular Detection
Center for Metabolic Bone Disease Histomorphometry and Molecular Analysis Core
Vision Science Research Center Histology Laboratory
High Resolution Imaging Facility
CMBD Small Animal Bone Phenotyping Core
Comprehensive Cancer Center Small Animal Imaging Shared Facility
Neuroscience Core - Behavioral Assessment
Transgenic Mouse Facility

Other facilities
Southern Research
AML Laboratories Research Histology Services (Rosedale MD)