I've added a lot of plugins to my server, but there's just one thing. I forget what plugins I have, since the /help list does not include them! I'm not sure if the /help list is default in Bukkit or it's from the Essentials plugin, but I really want to change the list of commands to add the new ones! I never had this problem with hMod as it'd always update the list, but Bukkit is looking like an equal replacement, especially at this stage.
There are a few plugins that provide the /help command, I personally use General, but I think Essentials does as well. The General plugin has a help configuration file where you can manually specify what commands do what. There's an OPTION in general for it to somehow automatically add commands; I've never used it but it can apparently get a bit ugly with that option set. Best bet is to manually add what you want to appear in /help.
I had the same problem. Use MCDocs plugin, it allows you to set the output to any command. You can make your own custom /help output (it also supports pages like /help 2, /help 3 etc.)
What do you mean by manually editing in the command? I can't seem to find any /help list in any of the files I've opened... with Essentials anyway. I don't think I have any other plugin that has edited /help tbh :/
With the General plugin, which is a watered-down Essentials, everything that shows up when you type /help in-game can be edited in a file named general.help. So when you add a new plugin, and you want to document the commands of that plugin for your users, you edit the general.help file to include that command along with a brief description. I looked through the documentation for Essentials and didn't see anything about being able to modify the /help info, perhaps that's not user-configurable output, but hard-coded with only Essential commands, or generated on-the-fly? As I said, I've never used that particular plugin, so I don't know how it works. You MAY need to either drop Essentials for another plugin to be able to edit your /help, or check with the author of Essentials to see if that's something that can easily be made configurable, if it's not already.