It recently came to my attention that MikuMikuDance, the program used to make most 3D Hatsune Miku PVs is now also available with a completely translated English interface.
English language subtitled instruction videos are also available.
Head over to the download page here.
EDIT 11/16/2012: The original developer of MMD ceased support for the software in 2011. The program still works and is widely used by many fans. However, a new alternative is available by the name of MikuMikuMoving. More info here: [Link]
EDIT 6/3/2013: MikuMikuDance was updated by its creator to version 7.39ｍ. More info here: [Link]