Where can I get a basic list of all permissions that I can deny/allow in PEX?
I am currently building my server, and I chose the PEX Bukkit plugin.
It is so far very easy to use. (Although I am a programmer, so any weird settings file that you have to edit using the command line hooked via SSH to your Raspberry Pi is easy.) That's not the point.
I have been wondering is there a Wiki or similar page that lists all the basic permissions in a fresh Bukkit install? I can easily get them for my mods mods; almost all of them are well supported and have a little section on their page. The ones that aren't I would never give away the power to use them "cough cough anti-greif." However I cannot find a simple list of the basic permissions that will be compatible with PEX.
What I want are things like "stop server" or "help" that are standard to Minecraft.
I believe you are referring to the permission nodes that are integrated into Bukkit already, such as /say, /plugin, /help, /stop, etc. You can find them all on the Bukkit Wiki, in a nice, organized table.
---------- Permission nodes for Bukkit ----------
bukkit.command.version - Gives the version number of the server.
bukkit.command.plugins - Lists all installed plugins on the server.
bukkit.command.reload - Stops and restarts all plugins on the server.
bukkit.command.timings - Records timings for all plugin events.
bukkit.command.tell - Allows the user to privately message another player.
bukkit.command.kill - Allows the player to kill themselves, returning to spawn.
bukkit.command.me - Says a message from the player's point of view (emote)
bukkit.command.help - Shows a list of server commands
bukkit.command.kick - Removes a player from the server.
bukkit.command.ban.player - Bans a player from the server.
bukkit.command.ban.list - Shows the banned players.
bukkit.command.unban.player - Pardons a banned player.
bukkit.command.ban.ip - Bans an IP address from the server.
bukkit.command.unban.ip - Pardons a banned IP address.
bukkit.command.op.give - Turns a player into a server operator.
bukkit.command.op.take - Removes server operator status from a player.
bukkit.command.teleport - Moves player to another player or coordinates.
bukkit.command.give - Gives player blocks/items
bukkit.command.stop - Gracefully stops the server
bukkit.command.save.perform - Forces a server-wide level save of the terrain.
bukkit.command.save.disable - Disables automatic terrain saving
bukkit.command.save.enable - Re-enables automatic terrain saving.
bukkit.command.list - Lists all currently connected players.
bukkit.command.say - Broadcasts a message to all players as the server.
bukkit.command.whitelist.enable - Enable whitelist (only listed players my join)
bukkit.command.whitelist.disable - Disable whitelist (all players may join)
bukkit.command.whitelist.add - Add a player to the whitelist
bukkit.command.whitelist.remove - Remove a player from the whitelist
bukkit.command.whitelist.list - Lists all currently whitelisted players.
bukkit.command.whitelist.reload - Reload the whitelist from file.
bukkit.command.time.add - Add to the world time.
bukkit.command.time.set - Set the world time.
bukkit.command.gamemode - Change the gamemode of a player.
bukkit.command.xp - Give player xp.
bukkit.command.toggledownfall - Turon on/off current weather.
bukkit.command.defaultgamemode - Change the gamemode of new players joining the server.
bukkit.command.seed - Outputs the world seed.
bukkit.command.enchant - Enchants the item in the user's hand.
bukkit.command.weather - Changes the weather in-game.
bukkit.command.clear - Clears a user's inventory.
bukkit.command.difficulty - Changes the difficulty of the Server.
bukkit.command.spawnpoint - Sets the spawnpoint of a specified user.
bukkit.command.gamerule - Displays current game rules.
bukkit.command.effect - Adds an effect to player.
bukkit.command.setidletimeout - Sets the servers idle timeout.
bukkit.command.setworldspawn - Sets a worlds's spawn point.
bukkit.command.achievement - Give user an achievement.
bukkit.broadcast.user - Allows the user to receive user broadcasts
bukkit.command.plugins - Allows user to look at plugins. Disables: /pl and /plugins
bukkit.command.ban - Combines the Player ban and the IP ban permissions
bukkit.command.unban - Combines the Player Unban and IP Unban permissions.
bukkit.command.op - Combines the Op Give and Op Take permissions.
bukkit.command.time - Combines the Time Add and Time Set permissions.
bukkit.command.save - Combines the Save Enable, Save Disable and Save Perform permissions.
bukkit.broadcast - Allows the user to receive all broadcast messages.
bukkit.broadcast.admin - Allows the user to receive administrative broadcasts.
Source: http://wiki.bukkit.org/CraftBukkit_Commands