http://www.youtube.com/user/PrefWakayama

Educational videos about the Wakayama Prefecture if you're interested.

Ken Tanaka's "How to speak fluent Japanese without saying a word":

Here's his channel:

http://www.youtube.com/user/helpmefindparents

Very funny. Not really much Japanese, tough. But he now has a Japanese channel, too:

http://www.youtube.com/user/kentanakajapan

My favorites were mostly flagged, but 鴨川ホルモー has some nice footage of Kyoto.

今大阪にも雪が降っています！

Walker Station TV

http://www.youtube.com/user/WSTV1

Narrated videos of hikes through World Heritage sites and along Japanese historic highways. I usually leave this running in the background at work. It looks like his most recent series will cover the first 10 temples of the 88 temple pilgrimage in Shikoku.

This guy has been keeping a log of every packaged noodle he's eaten for the last 13 years, and he has about 1000 of his reviews on YouTube. Best of all, the recent ones often have Japanese subtitles.
http://www.youtube.com/user/tontantin

http://www.youtube.com/user/shibuyalive
A channel by Josh Sehrer, an American who apparently visits Tokyo fairly often and gives insights into street life, skate boarding, clothing etc. I reckon his Youtube uploads are only a small fraction of what he has shot over the years.

Also noteworthy are his appearances on other channels:

http://www.youtube.com/tkyosam
Another channel by an American, named Sam, who lives in Tokyo and is in particular known for his 'Sam's Big in Japan' series http://www.youtube.com/tkyosam#g/c/9F6E5303CA918F27