I've spent a ton of time organizing my music files in iTunes, but not so much with music videos. The time I've spent trying to organize movie files has revealed to me that sub folders don't work. iTunes will ignore them. For example, I own all the Star Wars movies on DVD. I made iPhone friendly versions of them to sync to my phone as needed. Since iTunes ignored the neat little sub folder I put them in I had to resort to creative tagging. In this case, instead of their normal names, I named them SW1, SW2, etc, so they would show up in some sort of order.