This is a list of tools that I use for the making of Minecraft maps. They are all made by the Minecraft community, you can use them in complete safety. I use them for different tasks such as: create landscapes, custom mobs spawner, copy/paste structures or make custom equipments.
They are honestly great tools, but you may not need them all. I will try to show you what they can do but I can't be exhaustive. So I propose you a quick review of each one and informations about my personal use. In that way, you can have an idea of the possibilities of this tools by seeing what I've done on my own maps with them.
This software allow you to generate custom Minecraft maps. You can control the height and the type of terrain, the biomes, the underground ores and the caves. The "custom object layer" option give you the possibility to add the vegetation you want, using schematic files. All of that is done by simply painting: just as paint program, you use brush of different size and type to create your Minecraft world.
You can make a lot of various landscapes, and personally it's the main tool I use for the sceneries of my maps. Not too greedy in resources, regularly update and easy to use; it's the perfect software to make custom large worlds. I highly recommend to everyone to try it if you want to make custom map. WorldPainter Website
McEdit is a world editor. You can control the chunks, and also use schematics to copy and paste structures from a Minecraft world to an other. The different brushes features are helpful to quickly fill a place by a type of block, replace a type of block by an other. If you want to use the custom object layer option from WorldPainter, you will needs schematics and so McEdit.
My use of McEdit is limited to the copy/past of the villages and dungeons structures that I firstly made on a creative map. I also use it to make caverns and mines, by digging with a air brush. But one of the most interesting feature of McEdit is the use of filter, as Sethbling's ones. McEdit Website
McEdit can run filters, kind of plugins, to make more things. Sethbling is known to have wrote useful filters. The filters that he have wrote can make custom potions, custom trades for villagers or create geared mobs. He regulary wrote new filters, and explains how to use them in his youtube videos. Of course, you will need McEdit to use them.
I use his filters to make customs mobs and spawners in my dungeons, but also to make custom villager trades and custom items, like the godly ones in The Lands of Reminiscence. But it's a small part of all the filter he have wrote. If you want to make some special features on your map, take a look on his work. It will give you great tools for this. Sethbling Website
Chunky is a rendering tool creating photo realistic images of Minecraft world. You can set everything you need such as the texture pack you want, the canvas size, etc... The only downside of this program is that it's very CPU intensive. You will need a good computer, or be patient during the rendering.
Personally I have troubles with Chunky when I want to make large canvas. But it's a really good rendering program. The images that illustrate my website, like the banner, come from Chunky. A software to try if you want to make nice pictures of your Minecraft creations, but be sure that no other program is running if you have a low ressources computer like me. Chunky Wiki