Minecraft wiki entry for Development_resources, associated text: Minecraft Coder Pack used to create and edit mods to both the Minecraft client and server
MCAnimator - a modeler: used to create custom models which can have textures and animations. Has many tools to help you in the creation process. You can export to all the latest Minecraft versions. It has a library that allows perfect animations control.
Techne - the modeler: used to create custom models for in game use, comes with library of standard models.
FMCModeler can be used to create custom models for in game use, can also create models from Java code (with some restrictions). Written in Flash. It appears to be abandoned, but it's still working when used with CustomRenderer.