Help:
/aliases - opens this list
/readme - opens the readme

Selection:
/hpos1 - set the first position of your selection
/hpos2 - set the second position of your selection
/expand <direction> <amount> - expand selection along one axis
/expand <direction> -<amount> - contract selection along one axis
/inset - skrink selection in all directions
/outset - expand selection in all directions
/shift <direction> <amount> - move selection across one axis
/desel - deselect position

Region Operations:
/set <TileName> [dataValue] [oldBlockHandling] [dataTag] - gives you a fill command based on your selection
/clone [maskMode] [cloneMode] - gives you a clone command based on your selection
/setwalls <TileName> <dataValue> - set the walls of the selection
/setfloor <TileName> <dataValue> - fill the bottom of the selection
/setceil <TileName> <dataValue> - fill the top of the selection
/outline <TileName> <dataValue> - fill the edges of the selection

Navigation:
/up <distance> - teleports you up
/down <distance> - teleports you down
/waypoint <name> - create a waypoint
/waypoint <remove> <name> - delete waypoints
/goto <waypoint> - teleport to a waypoint
/goto <list> - list waypoints
/tpa <player> - teleport to a player

Utilities:
/killall <radius | all> - kill all nearby mobs
/killtype <entity> <radius | all> - kill a certain entity
/killname <name> <radius | all> - kill entities with a certain name
/killtag <name> <radius | all> - kill entities with a certain tag
/drain <radius> - drain nearby water
/ldrain <radius> - drain nearby lava
/removeabove <height> <radius> - remove blocks above your head
/removebelow <height> <radius> - remove blocks below your feet
/replacenear <radius> <from-id> <to-id> - replace all existing blocks nearby
/removenear <block> <size> - remove blocks near you
/void <radius> - delete the entire area
/room <radius> <TileName> <dataValue> - create a hollow box
/snow <radius> - cover area with snow
/thaw <radius> - remove snow
/burn <radius> - cover area with fire
/ex <radius> - extinguish fires
/flood <radius> <level> - floods your area and level with water
/lflood <radius> <level> - floods your area and level with lava
/sourceall <radius> - changes all flowing water to source water
/lsourceall <radius> - changes all flowing water to source water

Gamerule presets:
/nodrops - Disables all drop-related gamemodes
/maprules - Use a set of common map gamerules

Effect shortcuts:
/eclear - clear all active effects
/heal - heals your hp
/full - heal your hunger
/nohunger - toggle saturation
/bright - toggle night vision
/resistance - toggle resistance
/speed <level> - toggle speed
/haste - toggle fast block breaking in survival

Give shortcuts
/cmd - get a command block
/mcmd - get a minecart command block
/barrier - get a barrier

Gamemode shortcuts:
/c - creative mode
/s - survival mode
/a - adventure mode
/sp - spectator mode

Difficulty shortcuts:
/p - peaceful mode
/e - easy mode
/n - normal mode
/h - hard mode

Weather shortcuts:
/sun - weather clear
/rain - weather rain
/storm - weather thunder

Novelty shortcuts:
/boom - boom!
/boomboom - boomboom!!
/catboom - summon an exploding cat!
/meow - meow!
/himeow - meow!
/lomeow - meow!
/burp - burp!