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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.

Mammals

  • 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

  • Birds (any) - dissimulation, flock, flight (in air), volery (on ground)

Reptiles

Amphibians

Fish & Other Sea Life

  • Fish (any) - a draught, school, shoal

Insects

  • Insects (any) - swarm

And lastly...

Human Beings

  • 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.

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