A zoonosis is an infectious disease with an animal reservoir. The animal reservoir is usually another mammal or bird, but may also be an arthropod, which then doubles as a vector. Vector-borne diseases are not necessarily zoonoses! It is the natural reservoir that determines whether a disease is considered to be zoonotic.

Zoonotic diseases caused by bacteria

Disease Cause Reservoir
Anaplasmosis Anaplasma phagocyticum Small mammals
Anthrax Bacillus anthracis cattle
Bartonellosis (oroya fever) Bartonella bacilliformis wild animals
Botulism Clostridium botulinum various animals
Brucellosis Brucella spp. Goats, sheep, cattle, pigs, dogs
Campylobacteriosis Campylobacter jejuni Poultry, pigs, cats, dogs, rabbits, birds 
Cat Scratch Disease Bartonella henselae Cats
Ehrlichiosis (Monocytic) Ehrlichia chaffeensis Deer, rodents, dogs
Erysipeloid Erysipelothrix rhusiopathiae pigs, many other animals
Leptospirosis Leptospira interrogans Rodents, livestock, dogs, wild animals
Lyme Disease Borrelia burgdorferi Rodents, deer, pets, ticks
MAC disease Mycobacterium avium complex Birds, mammals
Plague Yersinia pestis Rats, squirrels, rabbits, pets
Psittacosis (parrot fever) Chlamydophila psittaci Birds
Q fever Coxiella burnetii Mammals, birds, ticks
Relapsing fever (endemic) Borrelia spp. Rodents, ticks
Rickettsialpox Rickettsia akari Rodents
Rocky Mountain Spotted Fever Rickettsia rickettsii Rodents, ticks
Salmonellosis Salmonella spp. Reptiles, birds, mammals
Scrub typhus Orientsia tsutsugamushi Rodents
Tularemia (rabbit fever) Francisella tularensis Rabbits, ticks, mammals, birds, fish
Typhus fever (endemic) Rickettsia typhi rodents
Typhus fever (epidemic) Rickettsia prowazekii flying squirrels, fleas, humans

Zoonotic diseases caused by viruses

Disease Cause Reservoir
Rabies Rhabdovirus
Ebola Filovirus
Marburg Filovirus
Lassa fever Arenavirus
Nipah & Hendra
Nairovirus hemorrhagic fever
Hantavirus PS
Rift Valley Fever Phlebovirus 
encephalitis Bunyavirus
West Nile
Yellow fever
Dengue fever
Cowpox poxviruses

Zoonotic diseases caused by protozoa

Disease Cause Reservoir
Babesiosis Babesia spp. Rodents
Balantidiasis Balantidium coli Pigs, monkeys
Cyclosporiasis Cyclospora cayetanensis Reptiles, birds, mammals
Toxoplasmosis Toxoplasma gindii Cats
African sleeping sickness Trypanosoma brucei rhodesiense game and domestic animals
Chagas disease Trypanosoma cruzi wild animals