General commands:

/afk: Marks you as away-from-keyboad
/butcher: Kill all or nearby mobs
/clearinventory: Clear all items in your inventory.
/fireball: Throw a fireball.
/firework: Allows you to modify a stack of fireworks.
/fly: Take off, and soar!
/hat: Get some cool new headgear. makes whatever is in your hand be your helmet (example: diamond block)
/kittycannon: Throw an exploding kitten at your opponent.
/lightning: The power of Thor. Strike at cursor or player.
/list: List all online players.
/near: Lists the players near by or around a player.
/nick: Change your nickname or that of another player.
/spawnpoint: A Mojang provided command.
/toggledownfall: A Mojang provided command.
/tp: Teleport to a player.
/tpa: Request to teleport to the specified player.
/tpaccept: Accepts a teleport request.
/tpahere: Request that the specified player teleport to you.
/tpdeny: Reject a teleport request.
/vanish: Hide yourself from other players.
/workbench: Opens up a workbench.

Teleport commands:

/back: Teleports you to your location prior to tp/spawn/warp.
/sethome: Set your home to your current location.
/home: Teleport to your home.
/jump: Jumps to the nearest block in the line of sight.
/top: Teleport to the highest block at your current position.
/warps: list available warps
/warp [warpname]: warp to the specified location.


Mail:
/mail: Manages inter-player, intra-server mail.
/mail send [playername] [message]: sends message via mail to a player
/mail read: read your mail
/mail clear: empty your mail

Chocolates:
/coco: Chocolates commands.

Disguises:
/d [mobtype]: Disguise yourself as a mob (example: /d rabbit)
/d player [minecraft player name]: disguises you as a player (example: /d player SuperGirlyGamer)
/undis: Undisguise.

Pets: 
/mypet: show all available MyPet commands.
/petinfo [username]
/petname [new-pet-name] :set the name of your MyPet.
/pcst: choose your pets skill
/petrelease [pet-name]: set your pet free
/petcall: teleport your pet to you
/petsendaway: send your pet away
/petstop: make your pet stop attacking someone.
/petinventory: see your pets inventory
/petbeacon: see your pets beacon settings
(you can only have one pet at a time)
(to get a pet: 1. leash a mob with a lead  2. punch the leashed mob with the lead)
(to ride your pet, leash it, then left click)