Copypasta:

Current best sites to find videos:
-nicovideo (search MMD, mikumikudance, and/or R-18)
-video.fc2 (mostly low quality for non members, but more edgy stuff, just don't post anything hentai here)
-toukoucity.to (a lot of porn, but still some tame stuff, so be careful what you link to. Also be mindful of duplicates. They seem to siphon mostly from fc2, but as it's easier to download and still of fair quality, it works.)
-Vimeo Dont know what to say about his now, it's not all gone, but a lot is.

Reminder: If you manage to gain access content by an artist that was hidden or protected, please respect their decision by not directly linking to it or giving out the passwords.

R-18 adjusted link to miterew, site that in much clearer format lists nicovideo videos:
http://mmd.miterew.com/Kiterew/f/TAG:7102/

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