As a quick list, I've always pointed people to the Top 20 list here on WarcraftPets:
[url]http://www.warcraftpets.com/wow-pets/top-twenty/[/url]
For more depth, I would look at a site or list of pets used in guides to tamer battles.
The most comprehensive guide site at the moment is [url]http://www.wow-petguide.com/[/url]. Looking around the various battles there, you will quickly see what pets are most commonly used.
For what it's worth, I just exported all my standard PvE teams covering Pandaria, Draenor, the Celestial Tournament, the Garrison, and general farming, from Rematch, and looked the pets up against my pets spreadsheet, and came up with the following lists of pets, and how many PvE teams I use each in. No doubt other people will have other distributions of pets, but I think I can recommend the top 40 or so to everyone. Some have preferred breeds, of course: P/P EPW and Crab and Nexus Whelpling, H/P Blighted Squirrel, P/B Anklerender for Tanaan and so on, but many have only one possible breed, so no confusion.
[pet]Nexus Whelpling[/pet] 12
[pet]Emerald Proto-Whelp[/pet] 12
[pet]Anubisath Idol[/pet] 11
[pet]Mechanical Pandaren Dragonling[/pet] 10
[pet]Chrominius[/pet] 8
[pet]Zandalari Anklerender[/pet] 8
[pet]Iron Starlette[/pet] 7
[pet]Pandaren Water Spirit[/pet] 7
[pet]Emperor Crab[/pet] 7
[pet]Darkmoon Tonk[/pet] 6
[pet]Sunreaver Micro-Sentry[/pet] 5
[pet]Blighted Squirrel[/pet] 5
[pet]Syd the Squid[/pet] 5
[pet]Clockwork Gnome[/pet] 5
[pet]Ghostly Skull[/pet] 5
[pet]Gilnean Raven[/pet] 5
[pet]Gilded Moth[/pet] 4
[pet]Dancing Water Skimmer[/pet] 4
[pet]Pterrordax Hatchling[/pet] 4
[pet]Xu-Fu, Cub of Xuen[/pet] 4
[pet]Unborn Val'kyr[/pet] 4
[pet]Molten Corgi[/pet] 4
[pet]Darkmoon Zeppelin[/pet] 4
[pet]Cornish Rex Cat[/pet] 3
[pet]Teroclaw Hatchling[/pet] 3
[pet]Infested Bear Cub[/pet] 3
[pet]Yellow Moth[/pet] 3
[pet]Core Hound Pup[/pet] 3
[pet]Rapana Whelk[/pet] 3
[pet]Feline Familiar[/pet] 3
[pet]Lil' Bling[/pet] 3
[pet]Bone Serpent[/pet] 2
[pet]Blackfuse Bombling[/pet] 2
[pet]Shimmershell Snail[/pet] 2
[pet]Highlands Turkey[/pet] 2
[pet]Warbot[/pet] 2
[pet]Ikky[/pet] 2
[pet]Eternal Strider[/pet] 2
[pet]Infinite Whelpling[/pet] 2
[pet]Spawn of Onyxia[/pet] 2
[pet]Amethyst Shale Hatchling[/pet] 2
[pet]Fossilized Hatchling[/pet] 2
[pet]Pebble[/pet] 1
[pet]Snarly[/pet] 1
[pet]Scourged Whelpling[/pet] 1
[pet]Yu'la, Broodling of Yu'lon[/pet] 1
[pet]Fjord Worg Pup[/pet] 1
[pet]Luyu Moth[/pet] 1
[pet]Crow[/pet] 1
[pet]Macabre Marionette[/pet] 1
[pet]Azure Whelpling[/pet] 1
[pet]Mechanical Axebeak[/pet] 1
[pet]Spring Rabbit[/pet] 1
[pet]Disgusting Oozeling[/pet] 1
[pet]Flayer Youngling[/pet] 1
[pet]Menagerie Custodian[/pet] 1
[pet]Leopard Tree Frog[/pet] 1
[pet]Mini Mindslayer[/pet] 1
[pet]Rotten Little Helper[/pet] 1
[pet]Mojo[/pet] 1
[pet]Sea Gull[/pet] 1
[pet]Terrible Turnip[/pet] 1
[pet]Slithershock Elver[/pet] 1
[pet]Viscidus Globule[/pet] 1
[pet]Hatespark the Tiny[/pet] 1
[pet]Bonkers[/pet] 1
[pet]Stitched Pup[/pet] 1
[pet]Wretched Servant[/pet] 1
[pet]Flamering Moth[/pet] 1
[pet]Elekk Plushie[/pet] 1
[pet]Ashwing Moth[/pet] 1
[pet]Enchanted Lantern[/pet] 1
[pet]Cerulean Moth[/pet] 1
[pet]Voodoo Figurine[/pet] 1
[pet]Mr. Bigglesworth[/pet] 1
[pet]Weebomination[/pet] 1
[pet]Netherspace Abyssal[/pet] 1
[pet]Arctic Fox Kit[/pet] 1
[pet]Enchanted Broom[/pet] 1
[pet]Pandaren Fire Spirit[/pet] 1
[pet]Blighthawk[/pet] 1
[pet]Lofty Libram[/pet] 1
[pet]Lesser Voidcaller[/pet] 1
[pet]Lifelike Mechanical Frostboar[/pet] 1