Part 01: Tools

There are a multitude of different 3D programs, but ultimately the one you end up with is up to you. If you don't have any experience in 3D, try dabbling with the free versions or demos while you learn. It'd be a waste of money to purchase software that you aren't going to use again.

3D Software (The Least You Need)

The best ones would be either Blender, Metasequoia, Maya or perhaps Lightwave in my opinion. Use anything that will allow you to edit mesh comfortably, and will export to DirectX 3D (.x) format. Once you've prepared the model, you will then be able to feed it through one of the special tools to prepare them for use in MMD.
*NOTE: Maya and Lightwave are both Pay to Use software. There are demos available but you won't be able to save, and the trials expire after about 30-40 days. It's easier to get Blender if you don't already own the full versions of either Maya, Lightwave, or 3DS Max if you have the luxury. Blender is free software that is just as capable as any of them for this purpose.*

Scripts & Plugins

  • PMX2Blender: The 'offspring' of PMD2Blender, this script set handles PMX files. Please note: there are multiple versions available for download.

  • PMD2Blender: A script set that allows you to import PMD models into blender, and to export them.
  • PMD Helper: This is built specifically for Lightwave. It allows you to export to PMD. There's a tutorial for using it here.

  • MQO Loader: Another one for Lightwave. This should enable you to import MQO models from Metasequoia.

  • Make Polygon: Based on the preview given, it looks to be the same as the 'Make Face' feature in blender, or the 'Create' in Metasequoia.

  • Morph Helper: This will help you create morphs and expressions. There are many more tools available for editing morphs, and some for UV.

  • Blend to Metaseq: I don't know how new this importer/exporter plugin is, but it seems to include the missing Gangu.dll file. Unfortunately I'm not aware of any special requirements the script may have at this time. If it doesn't work, i could only suggest setting Blender to run in Japanese (you can do so without changing the language of the interface.)

  • MMD Tool: This looks to be a new one for Cinema 4D users. I gather you can import, edit, and export models so long as you have the program.

Model Editing/Converting Tools

The first thing that you'll absolutely need is PMD Editor if you wish to edit the models you've made without the use of a (working) plugin. Otherwise, there are a few available that integrate into your existing software.
PMD Helper, which is a downloadable plugin, will help you to prepare and export bones, morphs (and more) all in one go. After running your file through PMD Helper, the only thing you really need to do is go into PMD Editor and add the credits that appear in the dialogue. That last step is optional, but you should credit yourself for your work, as well as the creators of the character you've made, if you don't use your own.

*NOTE: PMD Helper won't take triangulated mesh, so do your best to use Quads.*

For Blender, there's a PMD import/export script available, but there's a very large issue surrounding it. The script is built with python. Not only do you need to install both Blender AND Python, but you have to match the versions as well. Each version of Blender will only work with the version of Python that was released at the same time. Most of the scripts are very old, with little documentation on what version they were made with and when. You can still make models with blender, you may just want to export them and plug them through PMD editor the old fashioned way.

Lastly, the most popular alternative is Metasequoia. You can get it for free from the website.

*NOTE: For the latest versions, check the software website. Also please find out if the software is version specific, in case you need to update any tools and plugins along with it. Python and Blender are two such examples..*

PMD Editor / PMD Size Changer

PMD Editor is vital if you need to correct things on the fly, without having to plug it through the 3D program again. Especially since you may not have access to the plugins/software that others do. Generally, PMD Editor itself can do virtually everything but create the model.

Size changer is also helpful if you make your model too big, or too small by mistake. You can simply resize your model and save it as a copy of the original, and test it to see that it works as you want it to. The size of the model will directly affect the way it responds to loaded motion data.
Most downloaded motion data is made and saved on regular models, but the bones will move just as far on the smaller model as with the regular one. The result, little Miku will look like she's walking around in leaps and bounds. Big Miku will take teeny little steps. Put all 3 together and you'll have quite an act.