There's BDCraft Cubik Pro, which creates really nice models that can go in things such as mods and texture packs. I haven't done it in a long time, but it seems to work pretty well. However, I did hear about some issues when making animated models, but they can be circumvented.
Sadly, Cubik Pro isn't free, and requires a decent amount of experience to make animated 3D models (although static ones are pretty simple).
It is used by servers such as Mineplex (for minestrike texture packs), Hypixel, and for many mods.
(I just checked and it's renamed to Cubik Studio, which I assume is the newer and better version.)
