Current best sites to find videos:
-nicovideo - search MMD, mikumikudance, R-18, 紳士の社交場.
-video.fc2 - if you're really patient, or have plenty of money, there are good finds here.
-toukoucity.to - dodge the porn to get an /e/ MMD prize
-Vimeo - Grab them before they're gone
-Sita's site - trollvids.com - It's young, be gentle.
-soku - http://soku.youku.com/v?keyword=mmd - Chinito site


List of free apps/addons (google them) that might help you with downloading vids:
NicoFox
Downloadhelper
Freemake Video Downloader
JDownloader 2 beta