I was searching for a comprehensive list of Japanese kanji by frequency of use, and I managed to track down a list on Jonathan's Japan Journal. The list covers some 3,000 characters in order of frequency, with the data vaguely attributed to a now-dead link from Aichi University. While it's not quite the authoritative source I'd like to have, it looks like the real deal.
For any students of Japanese out there, you'll be quick to note that the list of daily use characters only has about 2,000, and even if you add in the additional name characters you only get a couple hundred in to the 2,000s. This list goes we'll beyond that, so if you're thinking about studying based on this list you may want to limit it to the first 2,000 or so.
And, for good measure, here's a frequency list for Chinese characters.