TuSKe

To create a custom enchantment, is very simple and easy to do, let's start with a simple tutorial.
After 1.5.3, you can create custom enchantments using effects in your skript. All you have to do is register a enchantment with a name, this name will be used at your code to enchant items.

on skript load:
     register a new custom enchantment with id name "Magic"

The id name is what you use in your code to enchants a item, in this example, we will use Magic as custom enchantment's name.

This is the basic of creating a custom enchantment, but it's not all. It has somethings that you can hide and the plugin will use a default value and there are values that are optional. The expressions that you don't need to set if you don't want are:

set max level of Magic to 10

The max level that a enchantment can have, it goes from 1 to 10, the default is 3.

set rarity of Magic to 3

The rarity of enchantment, it goes from 1 (rare) to 5 (common), the default is 3.

set accepted items for Magic to "Swords", "Bow" and "Armor"

The types of items that the enchantment accepts. This doesn't accept the ID or name of item, only especific values and they are:
Helmets, Chestplates, Leggings, Boots, Pickaxes, Axes, Shovels, Bow and Fishing Rod
And there are values that represents a group of groups above:
Tools: Pickaxes, Axes and Shovels
Armor: Helmets, Chestplates, Leggings and Boots
All: All groups above
If this option is not set, it will use the default value, All. You can use more than one value, it's just separate with "," or "and".

set enabled for Magic to true

If true, the enchantment can be gotten on enchantment table, else, only by skript. By default is false.

The optional value doesn't have a default value, so you don't need it if you don't want it.

set conflicts for Magic to Enchantment and Another_Enchantment

It will set a group of enchantments that is incompatible with the enchantment, it means that they won't be together at same item. The value is the ID name of other custom enchantments.

Here is a example of how it's should look like:

on skript load:
     register a new custom enchantment with id name "Magic"
     set {_enchantment} to "Magic" parsed as custom enchantment
     set max level of {_enchantment} to 5
     set rarity of {_enchantment} to 1
     set accepted items for {_enchantment} to "Swords" and "Bow"
     set lore name of {_enchantment} to "Magic Power"

After the configuration, you just have to reload the file: or you restart your server or you execute the skript effect:

reload all custom enchantments

If everything is right, you shouldn't see any errors on console. After that, you only have to create your custom effects for the enchantment by yourself. And to do that, you have some expressions to help you.

#You can specify the level or not.
%itemtype% has custom enchantment %custom enchantment%
level of custom enchantment %custom enchantment% of %itemstack%
#You can add or remove enchantments from it.
[all] custom enchantments of %itemstack%
...

To create a GUI, isn't that complex, we have these effects:

(format|create|make) [a] gui slot %numbers% of %players% with %itemstack% to [do] nothing

(format|create|make) [a] gui slot %numbers% of %players% with %itemstack% to close [using %click action% [(button|click|action)]]

(format|create|make) [a] gui slot %numbers% of %players% with %itemstack% to [close then] run %command sender% command %string% [as op] [using %click action% [(button|click|action)]] [with cursor [item] %itemstack%]

(format|create|make) [a] gui slot %numbers% of %players% with %itemstack% to [close then] run function %function% [using %click action% [(button|click|action)]] [with cursor [item] %itemstack% ]

The first one will do exactly nothing more than just nothing. The item won't peform any action.

The other 3 effects has [using %click action% ], if you use that in the effect, it will run the command/function only if it is a specifc click action. and if you don't want, it will run with any click type. The supported click actions are:

left, right, shift left, shift right, double click, middle, number key, drop and control drop

If you have v2.2-dev16b or above from Bensku' Skript fork, you will have to search for click action in its documentation, because the values are different.

The second will close when you click on it.

The last two has [with cursor %item stack% ]. It will only run if a player click on item, with another specific item.

The third will peform a command. You can execute with console or a player, and if it is a player, you can execute as op too.

And the last one is to execute a function.
Examples:

create a gui slot 0 of player with stone to do nothing
create a gui slot 1 of player with potato to close with left click
create a gui slot 2 of player with paper to run player command "CommandHere" as op
create a gui slot 3 of player with diamond to run console command "CommandHere"
create a gui slot 4 of player with gravel to run function giveItems(player) with cursor item stone

You can also use multiple action:

create a gui slot 2 of player with stone to run function subtract(1) with left click
create a gui slot 2 of player with stone to run function increase(1) with right click

If you want to change the item, you don't need to format the slot again, you can just change the item in slot:

function toggle(p: Player):
    if {var} is true:
        set slot 0 of current inventory of {_p} to red wool
    else:
        set slot 0 of current inventory of {_p} to green wool

#your code to open a inventory/virtual inventory
create a gui slot 0 of player with green wool to run function toggle(player)

And if you want to unformat the slot, it's just:

unformat the gui slot 1 of player
#or if you want the whole inventory
unformat all gui slots of player

And some conditions:

%player% has [a] gui #Check if has any gui in his open inventory
slot %number% of %player% is a gui #Check if a slot is a gui

Bug fixes from the old method, an another addon that it isn't update anymore:
- No wait a tick needed after open the inventory.
- It will only format the current open inventory of player (doesn't include the crafting slots).
- Doesn't conflicts with others slots of the same inventory.
- No loop problem, you can make loops and the command/function will have different values for each one.

on anvil combine:
      event-item-one is a diamond sword
      event-item-two is a diamond sword
      send "Oh, you combined two diamonds swords!"

on anvil rename:
      event-string is "Awesome axe"
      event-item-result is any axe
      send "You've renamed your %event-item% from %event-item's name% to %event-string%"

command /players: #will send a list of players in alphabetic order
      trigger:
            set {_players::*} to alphabet order of all players
            loop {_players::*}:
                  send "%loop-value%"

command /xp: #shows the amount of experiences orbs that player has
      trigger:
            send "You have %xp of player% experiences orbs."
on damage of player:
      if attacker's tool has custom enchantment Vampire:
            set {_AddHealth} to 1 * level of custom enchantment Vampire of attacker's tool
            add {_AddHealth} to health of attacker