One of my friends is a big fan of the kanji-learning method of James W. Heisig, in which you first memorize the meanings of all the characters, and then later go back and attempt to learn their readings. I'm pretty skeptical of this system of learning to read Japanese, for many of the reasons discussed by Nihongo PeraPera. It may be that those of us who first learned a few hundred kanji are a little more dubious of this strange method, and ascribe success students may have with it to enthusiasm and diligence.
But it has become popular on the Internet. Many people use it with specialized flashcard software, known as spaced repetition systems or SRS ( 1, 2, 3, 4 ). This is a component of the method of study championed by AJATT ( 1, 2 ) and others.
After reading about it on Omniglot the other day, I've been re-evaluating SRS. I've always read about is as part of learning the kanji Heisig's way. But it seems like a feasible way to memorize things, regardless of what you're trying to memorize.
There are a couple of open-source programs for SRS: Anki and Mnemosyne are the most notable ( 1, 2, 3 ). SuperMemo is Windows-only and reportedly very buggy, and my friend has used both smart.fm and Anki. I think I'd prefer to use Mnemosyne, but the latest client only runs on the Intel Macs. On first use, making a deck of flashcards is easy, but using it to organize a system of self-study is somewhat more complex and non-intuitive.
Rather than the Heisig method, I suspect sentence mining, perhaps something like Kanji in Context after starting with my trusty old "しんにほんごのきそ". I may try it with Interlingua or such first, to figure out how best to organize a deck.
I also suspect that while relying on flash cards may be an effective means of improving reading comprehension, it'd be a weaker method of developing fluency, listening comprehension, and other aspects of language proficiency. Of course with Japanese, where this method is most commonly used, vocabulary, literacy, and reading comprehension are very serious barriers to proficiency.