Well, I've received the first Heisig book and honestly, I have not made it past the first couple of pages. Why? Because I cannot bare to review a character without reference to its On and/or Kun-yomi reading(s), or at least examples of actual vocabulary usage. Instead, I find myself constantly wanting to look up characters I encounter, and many of the "mnemonic stories" I do not find particularly effective. I can definitely see how this would be a good series for the beginner, but in my case it was money not very well spent (In other words, I fell victim to the advertisers).
On a more positive note, a system which I have been using which has been rather effective is to use a flash-card program to study kanji-based vocabulary (As I mentioned in a prior post, I'm using Mnemosyne, which has the significant added benefit that you can download ready-made Japanese vocabulary lists for level 1-4 JLPT vocabulary, Japanese Surnames, etc. And its free.) When I encounter a kanji-based word which is particularly difficult to remember, or which contains highly unfamiliar characters, I refer to a kanji handbook (I use Kanji in Context) to look up the characters, and I also practice writing the characters in a notebook as well (I sometimes need to refer to a second character handbook for proper stroke order, etc.). When initially looking up characters, I do pay attention to alternative character readings (both On and Kun), as well as to other vocabulary which is constructed from those characters. However, I primary aim to associate the characters with the initial vocabulary in which I the characters were first encountered. This is simply to aid in my memorization of both the characters and the vocabulary, for it enables me to associate a particular character (or set of characters) with a particular vocubaluary word, and vice-versa. This is much more effective than simply trying to memorize arbitrarily.
In this way, I am able to learn kanji readings primarily through an up-down approach, in which I learn kanji readings through examples of their proper usage (Do be careful of irregular readings! For example, the following kanji for the word 'today,' 今日（きょうーkyou), contains neither 'on' or 'kun' readings. Such words are fairly common; the kanji serves to represent the meaning of the word alone, with no associated phonetic relationship (今＝now, this, etc.; 日＝day, sun, etc.).
I feel that this method of study is effective because it enables me both to study a variety of characters without being bogged down by the numerous 'on' and 'kun' readings associated with each character, and because it enables me to study both kanji and vocabulary at the same time, which seems far more efficient then studying each independently (as I use to do).
I will note that I do not believe this is by any means a complete course for Kanji study, but rather an effective exercise in kanji acquisition. I would say that it is still important to study individual characters, both for their form and for their readings, in addition to studying through this method. In addition, this method very much favors kanji reading ability, without much emphasis on writing. This may be enough if the goal is simply to learn to read [clearly written] kanji script, type proficiently in Japanese, and, possibly, to pass a multiple choice kanji exam, such as that found on the JLPT. However, to develop true kanji ability, it is necessary to learn how to properly write and identify each character. This impels one to acquire a host of addition abilities, including (but by no means limited to) etymological knowledge of Chinese characters, an understanding of proper stroke order, a knowledge of component elements, an ability to identify identical component elements appearing in various forms, and the muscular memory required to write each character (on account of this last point, it has been said that "writing Chinese is a skill of the arm.").
Personally, I have found myself heavily neglected my study of "how to write kanji" in favor of my study of "how to read kanji," largely because I have found that I am able to expose myself to a far greater number of characters by focusing on reading and recognition then I could by incorporating more writing; however my ability to write has definitely suffered as a result, and I am well aware that I am sacrificing my ability to know each character in depth for my ability to simply increase my reading ability at a rapid rate (and also for my ability to, I hope, prepare for the kanji section of this winter's level 2 JLPT - though the GRE may take precedent this year).
I hope this information is useful to some people. Personally, I am always learning new study techniques, and adapting my own methods, but this is one thing that I have found to be very effective lately.