You drag it into the plugins folder. If you want plugins in your minecraft server use bukkit, not the vanilla minecraft server.
Install bukkit
You need a server using Bukkit, and there are multiple plugins for it.
Bukkit is an API (application program interface) that changes the way plugins interact with the minecraft program. Most server mods will use Bukkit instead of attempting to 'hook on' to the actual minecraft software.
You go to BukkitDEV or Bukkit Plugin list. Then Download and take the .jar into the plugins Also, some come with folders so put the folder in the plugins folder aswell. *Note* You need a Bukkit server for this.
Download the latest CraftBukkit server from bukkit.org(top-right corner of the home page). For plugins, click on 'Get Plugins'.
You'll need Bukkit. There are various plugins; I use PermissionsEx
instead of using the jar file from the minecraft website get one called craft bukkit you can find a million tutorial on craft bukkit just use google or youtube
Bukkit is an Minecraft Server Hosting software.
It's pretty easy. You're gonna need a Minecraft BUKKIT Server, just search 'Bukkit' in your browser. Once it's all set up, go into your server folder then go into the 'Plugins' folder. Which is obviously MobDisguise, then drag the ZIP into your 'Plugins' folder. Now run your server and enjoy!
You can't... To make a server that can use plugins, you setup a Bukkit server from their website... it's not possible to put plugins on the Minecraft_Server.exe type servers (not currently anyway)
Go on bukkit plugins and get a saving program that should help it and if it doesn't work re-install the server files.