I wrote a program to generate customizable heightmaps. It is written in Java. You can download it here.

This program works by taking multiple layers of terrain zoomed to different levels and combines them. One layer could be hills, another one for boulders, etc.

Here is a description of the parameters available:

1. Octaves: The number of layers to be combined. A larger number gives more complex terrain.
   
2. Persistence: The strength of each layer. The strength of each layer decreases as more and more are added; this parameter determines how fast it decreases.
   
3. Frequency: How zoomed in the heightmap is. Lower values give flatter, smoother terrain.
   
4. Exponent: The exponent to which the heightmap is raised. Higher values give more contrasting (spiky) terrain; low values give a boring terrain.
   
5. Offset: How much the terrain is offset from zero.
   
6. Render: Update the heightmap viewing window.
   
7. Save: Save the contents of the heightmap viewing window to a file named "output.png"
   

..and on the Filters window:

1. Island: Generate an island.
   
2. Terracing: Split the landscape into terraces.
   
3. Terraces: The number of terraces. A larger number means coarser landscape.
   
4. Colorful Render: Whether the heightmap should be colorful or not.
   
5. Water Level: The level at which water is present. This is only applied with the Colorful Render.
   

You can convert the heightmap into a Minecraft world with tools like WorldPaint.

This program is free, and you can use it for whatever you want (or distribute it) as long as you credit me and it stays under these terms.

EDIT: Updated, added the Colorful Render feature