This page has a list of commands and a more in-depth description and how to use them properly.
The commands are listed in default rank setup, Starting with SuperOp, down to the measly banned
 SuperOp Commands
SuperOp can control everything, so be carful when you assign one.
|/botadd [name]||Where [name] is the name of the bot you want to add.||Makes a bot||no image|
|/botremove [name]||Where [name] is the name of the bot to remove.||The bot you want to remove must be in the same level as you.||no image|
|/botsummon [name]||Where [name] is the name of the bot you want to summon.||Brings the bot to you!||no image|
|/clearblockchanges||No variables. You can use this on the map you are on.||Clear Block Changes removes all block changes from the MySQL database, Which makes map loading and the /about command a lot faster.||no image|
|/banip [full_username]||Where [full_username] is a players full username that you are banning.||This command bans a user IP address. Use very carefully.||no image|
|/deletelvl [levelname]||Where [levelname] is the level's name you want to delete.||When you are deleting a level, no one can be on it. It moves the map in to a "deleted" folder.||no image|
|/limit [rank] [buildlimit]||Where [rank] is the rank you are editing, [buildlimit] is the amount of commands the rank can use per player.||/limit changes the limit for "/rp finite" and /limit changes the limit for "/rp"||no image|
|/newlvl [mapname] [x] [y] [z] [type]||Where [mapname] is the map's name you want. [x][y][z] is the size. [type] is the type of map.||All of the xyz parameters must me in a power of two (16, 32, 34, 128, 256, 512, 1024). The ideal size is 256 by 64 by 256. The valid types of maps are flat, island, forest, ocean†, mountain, pixel and desert.||no image|
|/renamelvl [levelname] [newname]||Where [levelname] is the old name of a level, and [newname] is the level's new name.||All portals going to and from the level will not work after renaming the level||no image|
|/replaceall [type1] [type2]||Where [type2] is the block to replace [type1]||See MCzall#Default_blocks supported blocks||no image|
|/serverreport||none||Shows the server's report.|
|/title [player] [title]||Where [player] is a player's username and [title] is the title for the player.||If no [title] is given, then [player]'s title will be removed.||no image|
† Although it is listed, the MCzall page doesn't have it under newlvl.
 Operator+ Commands
Operators are more like a moderator, they can’t make a new level, but they can ban and kick users, along with a list of commands.