Java?
Off topic → Programming → Java?
Are you talking about making Minecraft or Bukkit plugins? The best to get started with would be Bukkit plugins either way, since making those involves less work. To get started, I would recommend getting a Java book of some sort and possibly watch a few tutorials on how to make Bukkit plugins just to get you started. Most of the people who makes these tutorials don’t have great coding practises and thus make you learn bad habits. Stop with watching them as soon as possible. Most of these tutorial series start with how to set up Eclipse (an IDE/Integrated Development Environment) as well.
There are no ‘special’ programs involved as you’re just writing plain old Java code that Bukkit loads and executes.
By the way @redstone_sheep, how is Java a pain to work with when using libraries? I als wouldn’t use Maven when just starting to be honest. Maven is particularly useful for managing a lot of libraries, although it makes life a bit easier if you know how to use it, for smaller projects!