In battle.net (via local chat or whisper at any time):

!addadmin <name> add a new admin to the database for this realm
!addban <name> [reason] add a new ban to the database for this realm
!announce <sec> <msg> set the announce message (the bot will print <msg> every <sec> seconds in the lobby), use "off" to disable the announce message
!autohost <m> <p> <n> auto host up to <m> games, auto starting when <p> players have joined, with name <n>, use "off" to disable auto hosting
!autostart <players> auto start the game when the specified number of players have joined, use "off" to disable auto start
!ban alias to !addban
!channel <name> change battle.net channel
!checkadmin <name> check if a user is an admin on this realm
!checkban <name> check if a user is banned on this realm
!close <number> ... close slot
!closeall close all open slots
!countadmins display the total number of admins for this realm
!countbans display the total number of bans for this realm
!deladmin <name> remove an admin from the database for this realm
!delban <name> remove a ban from the database for all realms
!disable disable creation of new games
!enable enable creation of new games
!end <number> end the specified game in progress (disconnect everyone)
!exit [force] shutdown ghost++, optionally add [force] to skip checks
!getclan refresh the internal copy of the clan members list
!getfriends refresh the internal copy of the friends list
!getgame <number> display information about a game in progress
!getgames display information about all games
!hold <name> ... hold a slot for someone
!hostsg <name> host a saved game
!load <filename> load a config file (for changing maps), leave blank to see current map - the ".cfg" is automatically appended to the filename
!loadsg <filename> load a saved game
!map <filename> alias to !load
!open <number> ... open slot
!openall open all closed slots
!priv <name> host private game
!privby <owner> <name> host private game by another player (gives <owner> access to admin commands in the game lobby and in the game)
!pub <name> host public game
!pubby <owner> <name> host public game by another player (gives <owner> access to admin commands in the game lobby and in the game)
!quit [force] alias to !exit
!say <text> send <text> to battle.net as a chat command
!saygame <number> <text> send <text> to the specified game in progress
!saygames <text> send <text> to all games
!sp shuffle players
!start [force] start game, optionally add [force] to skip checks
!stats [name] display basic player statistics, optionally add [name] to display statistics for another player (can be used by non admins)
!statsdota [name] display DotA player statistics, optionally add [name] to display statistics for another player (can be used by non admins)
!swap <n1> <n2> swap slots
!unban alias to !delban
!unhost unhost game in lobby
!version display version information (can be used by non admins)

In game lobby:

!a alias to !abort
!abort abort countdown
!addban <name> <reason> add a new ban to the database (it tries to do a partial match)
!announce <sec> <msg> set the announce message (the bot will print <msg> every <sec> seconds), leave blank or "off" to disable the announce message
!autostart <players> auto start the game when the specified number of players have joined, leave blank or "off" to disable auto start
!autosave <on/off> enable or disable autosaving
!ban alias to !addban
!check <name> check a user's status (leave blank to check your own status)
!checkban <name> check if a user is banned on any realm
!checkme check your own status (can be used by non admins, sends a private message visible only to the user)
!close <number> ... close slot
!closeall close all open slots
!comp <slot> <skill> create a computer in slot <slot> of skill <skill> (skill is 0 for easy, 1 for normal, 2 for insane)
!compcolour <s> <c> change a computer's colour in slot <s> to <c> (c goes from 1 to 12)
!comphandicap <s> <h> change a computer's handicap in slot <s> to <h> (h is 50, 60, 70, 80, 90, or 100)
!comprace <s> <r> change a computer's race in slot <s> to <r> (r is "human", "orc", "night elf", "undead", or "random")
!compteam <s> <t> change a computer's team in slot <s> to <t> (t goes from 1 to # of teams)
!dl <name> alias to !download
!download <name> allow a user to start downloading the map (only used with conditional map downloads, it tries to do a partial match)
!from display the country each player is from
!hold <name> ... hold a slot for someone
!kick <name> kick a player (it tries to do a partial match)
!latency <number> set game latency (50-500), leave blank to see current latency
!lock lock the game so only the game owner can run commands
!mute <name> mute a player (it tries to do a partial match)
!open <number> ... open slot
!openall open all closed slots
!owner [name] set game owner to yourself, optionally add [name] to set game owner to someone else
!ping [number] ping players, optionally add [number] to kick players with ping above [number]
!priv <name> rehost as private game
!pub <name> rehost as public game
!refresh <on/off> enable or disable refresh messages
!sendlan <ip> [port] send a fake LAN message to IP address <ip> and port [port], default port is 6112 if not specified
!sp shuffle players
!start [force] start game, optionally add [force] to skip checks
!stats [name] display basic player statistics, optionally add [name] to display statistics for another player (can be used by non admins)
!statsdota [name] display DotA player statistics, optionally add [name] to display statistics for another player (can be used by non admins)
!swap <n1> <n2> swap slots
!synclimit <number> set sync limit for the lag screen (10-10000), leave blank to see current sync limit
!unhost unhost game
!unlock unlock the game
!unmute <name> unmute a player (it tries to do a partial match)
!version display version information (can be used by non admins, sends a private message visible only to the user)
!virtualhost <name> change the virtual host name
!votecancel cancel a votekick
!votekick <name> start a votekick (it tries to do a partial match, can be used by non admins)
!yes register a vote in the votekick (can be used by non admins)

In game:

!addban <name> <reason> add a new ban to the database (it tries to do a partial match)
!autosave <on/off> enable or disable autosaving
!ban alias to !addban
!banlast <reason> ban the last leaver
!check <name> check a user's status (leave blank to check your own status)
!checkban <name> check if a user is banned on any realm
!checkme check your own status (can be used by non admins, sends a private message visible only to the user)
!drop drop all lagging players
!end end the game (disconnect everyone)
!from display the country each player is from
!kick <name> kick a player (it tries to do a partial match)
!latency <number> set game latency (50-500), leave blank to see current latency
!lock lock the game so only the game owner can run commands
!mute <name> mute a player (it tries to do a partial match)
!muteall mute global chat (allied and private chat still works)
!owner [name] set game owner to yourself, optionally add [name] to set game owner to someone else
!ping ping players
!stats [name] display basic player statistics, optionally add [name] to display statistics for another player (can be used by non admins)
!statsdota [name] display DotA player statistics, optionally add [name] to display statistics for another player (can be used by non admins)
!synclimit <number> set sync limit for the lag screen (10-10000), leave blank to see current sync limit
!unlock unlock the game
!unmute <name> unmute a player (it tries to do a partial match)
!unmuteall unmute global chat
!version display version information (can be used by non admins, sends a private message visible only to the user)
!votecancel cancel a votekick
!votekick <name> start a votekick (it tries to do a partial match, can be used by non admins)
!yes register a vote in the votekick (can be used by non admins)

In admin game lobby:

!addadmin <name> <realm> add a new admin to the database for the specified realm (if only one realm is defined in ghost.cfg it uses that realm instead)
!autohost <m> <p> <n> auto host up to <m> games, auto starting when <p> players have joined, with name <n>, use "off" to disable auto hosting
!checkadmin <name> <realm> check if a user is an admin for the specified realm (if only one realm is defined in ghost.cfg it uses that realm instead)
!countadmins <realm> display the total number of admins for the specified realm (if only one realm is defined in ghost.cfg it uses that realm instead)
!deladmin <name> <realm> remove an admin from the database for the specified realm (if only one realm is defined in ghost.cfg it uses that realm instead)
!disable disable creation of new games
!enable enable creation of new games
!end <number> end a game in progress (disconnect everyone)
!exit [force] shutdown ghost++, optionally add [force] to skip checks
!getgame <number> display information on a game in progress
!getgames display information on all games
!hostsg <name> host a saved game
!load <filename> load a config file (for changing maps), leave blank to see current map - the ".cfg" is automatically appended to the filename
!loadsg <filename> load a saved game
!map <filename> alias to !load
!password <p> login (the password is set in ghost.cfg with admingame_password)
!priv <name> host private game
!privby <owner> <name> host private game by another player (gives <owner> access to admin commands in the game lobby and in the game)
!pub <name> host public game
!pubby <owner> <name> host public game by another player (gives <owner> access to admin commands in the game lobby and in the game)
!quit [force] alias to !exit
!saygame <number> <text> send <text> to the specified game in progress
!saygames <text> send <text> to all games
!unhost unhost game