See also: All PEX Commands

pex	display help
pex reload	reload permissions
pex user <user> group set <group> [world]	assign <user> to <group> (removing him from all other groups)
pex group <group> users	list all users in <group>
pex group <group> add <perm> [world]	add <perm> to <group> in optional [world]
pex group <group> list [world]	list all permissions assigned to <group> in optional [world]
pex user <user> list [world]	list all permissions assigned to <user> in optional [world]
pex users	list out all the registered users
pex groups	list out all the registered groups
pex hierarchy	print complete user/group hierarchy
pex user <user> check <perm>	check if <user> has specified <perm>
pex user <user> delete	remove <user> from permissions file

CraftBukkit is a bootleg Minecraft server.  There's no official download now for the builds.  Bukkit.Org used to have daily builds on GitHub but they got their asses kicked by Mojang and had to take it offline.  My interest in the CraftBukkit server was due to wanting an anti-griefing plugin for my home server.

Here's where it explains how to set up a CraftBukkit server among other things:
http://wiki.bukkit.org/Main_Page

First off, here's where I got the compiled CraftBukkit 1.8.8 jar:
http://maven.elmakers.com/repository/org/bukkit/craftbukkit/

1) I downloaded the 1.8.8 build and saved it in my ~/CraftBukkit folder.

4) Edit the eula.txt file and set the variable in there to true.

Ok here are some links related to CraftBukkit configuration:
Wiki:
http://wiki.bukkit.org/Main_Page
Forums:
https://bukkit.org/forums/
Commands:
http://wiki.bukkit.org/CraftBukkit_Commands
Command Line Options:
http://wiki.bukkit.org/CraftBukkit_Command_Line_Arguments
Permissions:
(About the file) http://wiki.bukkit.org/Permissions.yml

(bPermissions plugin) http://dev.bukkit.org/bukkit-plugins/bpermissions/

    look for bChatManager too, it's for color coding chat text

Download plugins and put them in the /plugins folder of your CraftBukkit server folder.

Here's the list of plugins:
http://dev.bukkit.org/categories/

Recommended Plugins:
http://www.bestplugins.com/articles/minecraft-bukkit-plugins

Active development for CraftBukkit 1.8.x:
Admin Tools
http://dev.bukkit.org/bukkit-plugins/vault/
http://dev.bukkit.org/bukkit-plugins/essentialsx/  (this should give you the /sethome and /home commands)

http://dev.bukkit.org/bukkit-plugins/title-welcome-message/
http://dev.bukkit.org/bukkit-plugins/olls-minecraft-server-gui/
http://dev.bukkit.org/bukkit-plugins/population-density/
http://dev.bukkit.org/bukkit-plugins/rtp-bukkit/  (random teleport)
http://www.curse.com/bukkit-plugins/minecraft/worldedit  (make blueprints, modify terrain, more!)
http://dev.bukkit.org/bukkit-plugins/easyranks/ (color coded ranks in player list, set player rank command for ops)

Cool Stuff
http://www.curse.com/bukkit-plugins/minecraft/realms

Here's what I have installed:

Allows claiming land for yourself and protecting your property against explosions, floods, robbery, etc.
Documentation:

(General) http://dev.bukkit.org/bukkit-plugins/grief-prevention/

(Admins) http://dev.bukkit.org/bukkit-plugins/grief-prevention/pages/how-to-guide-for-administrators/

(Commands and Permissions) http://dev.bukkit.org/bukkit-plugins/grief-prevention/pages/command-and-permissions-reference/
Download: http://dev.bukkit.org/bukkit-plugins/grief-prevention/

/plugins/GriefPrevention.jar

This is an API for other plugins to access permissions, economy functions and more.

After installing, you might want to opt out of server info broadcasting by setting opt-out: true in
/plugins/Plugin Metrics/config.yml

Other plugins that use Vault: http://dev.bukkit.org/bukkit-plugins/vault/pages/using-vault/  (economy plugins might be interesting)

Download: http://dev.bukkit.org/bukkit-plugins/vault/  (see forum for more info)

/plugins/Vault.jar

WorldEdit (1.8.1 up to 1.8.8)
WorldEdit is an easy-to-use in-game world editor for Minecraft, supporting both single player and multiplayer.

Documentation: http://wiki.sk89q.com/wiki/WorldEdit

Download: http://www.curse.com/bukkit-plugins/minecraft/worldedit  (orange download button)

/plugins/WorldEdit.jar

Gives you the /sethome and /home commands

Documentation:

(Command Reference) http://wiki.mc-ess.net/wiki/Command_Reference

(Starter Kits)
http://wiki.ess3.net/wiki/Kits
http://wiki.ess3.net/wiki/Item_Meta (tells how to do custom books in starter kits, too)

http://minecraft-ids.grahamedgecombe.com/ (Item IDs - gold shovel is 284 for claims)

(Sign Documentation) http://wiki.mc-ess.net/wiki/Sign_Tutorial

(Tutorials) http://ess.khhq.net/wiki/Tutorials

https://github.com/drtshock/Essentials/wiki

/plugins/EssentialsX-2.0.1.jar

Shows the prefixes and suffixes in chat.  The plugin comes with the EssentialsX pack.

Configuration: http://wiki.ess3.net/wiki/Chat_Formatting

/plugins/EssentialsXChat-2.0.1.jar

Manage player command permissions, promote players to op via command line in-game, etc.

Documentation:
https://github.com/PEXPlugins/PermissionsEx/wiki
Download:
http://dev.bukkit.org/bukkit-plugins/permissionsex/

Show claims on your Dynmap
/jdgp reload - to reload the configuration file.

/jdgp - for list of all commands related to the plugin

admin permission: jdynmapgriefprevention.admin (to see all available commands)

Documentation and Download:
https://www.spigotmc.org/resources/jdynmapgriefprevention.818/

See also (original very slow Dynmap-GriefPrevention plugin): http://dev.bukkit.org/bukkit-plugins/dynmap-griefprevention/

Limit your players to a specific region.  World border is shown on DynMap.

Download: http://dev.bukkit.org/bukkit-plugins/worldborder/

Permissions and Commands:

http://dev.bukkit.org/bukkit-plugins/worldborder/pages/commands-and-permissions/

Set all permissions for admin group:  /pex group admin add worldborder.*

/wb = list available WorldBorder commands

Used for things like FramePicture (FramePicture only available for Spigot 1.8.1... bleh, whaahhh!)

Permissions:

protocol.admin - enable administrative commands

Commands:

Here's where you can get Minecraft decompiled source code:
http://theunknownhosting.tk/minecraft/build/

Here's where you can get the latest Bukkit.jar API build:
https://hub.spigotmc.org/nexus/content/groups/public/org/bukkit/bukkit/