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 (the English site that has been hosting more MMD content by the month now with Japanese seasonings.)

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

For some time, I thought the NicoVid redesign had killed what was left of the MMD community. Seems I was wrong.

sm22329875 <--- Image source, but the next has some too.
sm22310638

These give me hope.