Here is a rather exhaustive list. Many of these terms originated from European hunting terminology, which explains the preponderance of European species and the wide variegation among the birds. Many of the terms first appeared in print in The Book of St. Albans, a treatise on hawking, hunting, and heraldry published in 1486.
- Antelope - a herd
- Apes - a band, pack, shrewdness
- Asses - a pace
- Baboons - a congress, flange, pack, tribe
- Badgers - a cete, colony
- Bats - a colony, swarm
- Bears - a den, sloth, sleuth
- Beavers - a colony, lodge
- Bison - a herd
- Boar - a herd, singular, sounder
- Bucks - a crash
- Buffalo - a gang, herd, an obstinacy
- Camels - a flock, herd
- Cats - a clowder, clutter, destruction (wild cats), dout (house cats), glaring, nuisance (house cats), pounce
- Cattle - a drove, herd, kine, team
- Chamois - a herd
- Chimpanzees - a band, cartload, pack
- Chinchillas - a herd
- Cows - a flink (12 or more)
- Coyotes - a band
- Colts - a rag, rake
- Curs - a cowardice
- Deer - a herd, leash, parcel
- Dogs - a kennel, pack
- Dolphins - a pod, school
- Donkeys - a drove, herd, pace
- Elephants - a herd, memory, parade
- Elk - a gang, herd
- Ferrets - a cast, business, fesnying
- Foxes - a lead, leash, skulk, earth
- Gerbils - a hoard
- Giraffes - a corps, herd, tower
- Gnus - a herd, implausibility
- Goats - a drove, herd, tribe, trip
- Gorillas - a band
- Greyhounds - a leash
- Guinea pigs - a group
- Hamsters - a horde
- Hares - a drove, down, husk, leap, leash, trace, trip, warren
- Hedgehogs - an array, a prickle
- Hippopotami - a bloat, crash, herd
- Hogs - a drift, parcel, passel
- Horses - a harras, herd, stable or stud (when belonging to a single owner), team, troop
- Hounds - a cry, mute, pack
- Hyenas - a cackle, clan, pack
- Kangaroos - a herd, mob, troop
- Kittens - an intrigue, a kendle, kindle, litter,
- Leopards - a leap
- Lions - a pride, sault, sowse, troop
- Llamas - a herd
- Mares - a stud
- Marmots - a madness
- Mice - a horde, mischief, nest
- Moles - a company, labor, movement
- Monkeys - a band, barrel, cartload, pack, tribe, troop, troupe
- Moose - a herd
- Mules - a barren, pack, rake, span, team
- Otters - a bevy, family, raft, romp
- Oxen - a drove, herd, span, team, yoke (two)
- Pigs - a drift, drove, herd, team
- Piglets - a farrow, litter
- Polar Bears - an aurora, a pack
- Polecats - a chine
- Ponies - a string
- Porcupines - a prickle
- Porpoises - a pod, school
- Possum - a passel
- Prairie dogs - a coterie
- Puppies - a litter
- Rabbits - a bury, colony, down, drove, herd (domestic only), hush, leash, nest (young), trace, trip, warren, wrack (young)
- Raccoon - a gaze, nursery
- Rats - a colony, horde, mischief, pack, plague, swarm
- Rhinoceri - a crash
- Roebuck - a bevy
- Seals - a bob, colony, crash, harem, herd, pod, rookery, spring, team
- Sheep - a down, drove, flock, fold, herd, hurtle, trip
- Squirrels - a dray, scurry
- Swine - a drift, sounder
- Tigers - an ambush, a streak
- Wallabees - mob
- Walruses - a herd, pod
- Weasels - a pack, sneak
- Whales - a gam, herd, pod, school
- Wolves - a pack, rout
- Wombats - a warren
- Yaks - a herd
- Zebra - a herd, zeal
- Birds (any) - dissimulation, flock, flight (in air), volery (on ground)
- Bitterns - a sedge, siege
- Buzzards - a wake
- Bobolinks - a chain
- Chicks - a brood, chattering, clutch
- Chickens - a brood, peep
- Chough - a chattering
- Coots - a cover
- Cormorants - a gulp
- Cranes - a sedge, siege
- Crows - a murder, storytelling
- Curlew- a herd
- Doves - a bevy, cote, dule, dole, flight, pitiousness, prettying
- Dotterel- a trip
- Ducks - a flush (when flushed), paddling, raft, suite, team
- Dunlin- a fling
- Emus - a mob
- Eagles - an aerie, a convocation
- Falcons - a cast
- Finches - a charm, trembling
- Flamingos - a stand (standing)
- Geese - a gaggle or skein (on the ground), wedge (in flight)
- Gosling - a skein
- Grouse - a covey, pack
- Guillemots - a bazaar
- Gulls - a colony
- Hawks - an aeire, a boil (when circling), cast, kettle
- Hens - a brood
- Herons - a hedge, sedge, siege
- Hummingbirds - a charm
- Jays - a band, party, scold
- Larks - an ascension, exaltation
- Lapwings - a deceit, desert
- Magpies - a charm, chattering, gulp, murder, tiding, tittering
- Mallards - a sord
- Martens - a richness
- Nightingales - a watch
- Owls - a parliament
- Parrots - a company, pandemonium
- Partridges - a covey
- Peacocks - a muster, an ostentation
- Penguins - a colony, crèche, huddle, parcel, rookery
- Pheasants - a bouquet (when flushed), covey, head, nest, nide or nye (when on the ground)
- Pigeons - a kit
- Pintail - a raft
- Plovers - a congregation, wing (in flight)
- Pochards - a rush
- Ptarmigans - a covey
- Quail- a bevy, covey, drift
- Ravens - a conspiracy, an unkindness, a storytelling
- Rooks - a building, clamor, parliament, rookery, storytelling
- Ruffs - a hill
- Sheldrake - a dopping
- Snipe - a walk, wisp
- Sparrows - a host, quarrel
- Starlings - a chattering, murmuration
- Storks - a mustering
- Swans - a bevy, herd, lamentation, wedge
- Teal- a spring
- Turkeys - a brood (young), gang, rafter
- Turtledoves - a dule, pitying
- Thrushes - a mutation
- Vultures - a colony
- Widgeons - a company, trip
- Wildfowl - a plump
- Woodcocks - a fall
- Woodpeckers - a descent
- Wrens - a herd
Fish & Other Sea Life
- Fish (any) - a draught, school, shoal
And lastly...
- Humans - army, civilization, clan, company, corporation, country, crowd, culture, group, nation, race, society, tribe
Sources include:
http://www.bellaonline.com/articles/art13151.asp;
http://rinkworks.com/words/collective.shtml;
an E2 writeup by the inimitable Footprints;
The OED; and
my own knowledge.