I apologize for bumping a semi-old thread with lots of good resources, but I believe I can add to this.
First, I do not believe in overloading the brain. I study one thing at a time, and by that I mean Speaking/Hearing is one thing, Writing is another, etc. This is because you can study 2 separate parts faster than one whole one. If I tried to speak and remember the Kanji for what I said, I'd take forever. So I ignore the pdf's until AFTER I've gone through the lesson.
Some backstory. I study foreign languages for fun. In retail, I needed to stay sharp. Now I'm a programmer. I do process, product, efficiency. That said, I find Kanji to be strange. We can express every single noise in 26 characters, but you need 2136 in Japan. For a programmer, this is inefficient. But that's just a bit of autistic-ish humor. Five years ago, I realized I was never going to write unless I was forced, so I took a year in undergrad college. We started with Kana and 3rd quarter introduced Kanji. (don't worry, I'll get to the non-college beginner way still).
In College we had the ability to use what we learned. Writing fake Journal entries, responding to the teacher, Nakama 1 was our workbook to go through, review, etc. We learned through rote memorization and repetition (yucky), but interaction also.
Skip ahead to now, where I forgot how to read and write everything except Day, Watashi, and a few others. However, I can watch a show and get nearly half of it without words. Granted, I don't know many specific words. I'm tearing up every bookstore looking for "workbooks" that give you the interaction needed. I found one, Tokyo U's 250 Essential Japanese Kanji books, 2 volumes. My 2 criteria are "Write it, over and over" and "Not too many at once".
Every flashcard program seems to have the fatal flaw of "Let's present all 2000 and just repeat the ones they don't know!" Yeah, awesome, whose brain can hold that much? Even if they do manage a bit, you just tore open their neural pathways by burning through their memory ability.
Eventually I find 2 awesome resources. The first is Scribe Origins (not Scribe Japanese - I don't think it's as easy), the only Flashcard app that actually presents a few at a time, then waits until you master it and presents some more. Sound slow? It's not. If you take an extra 10 minutes to completely master 10 Kanji, then only 10 minutes for another, within an hour you have 100 Kanji memorized and solid. You get the repetition and the feedback without the overload. Yes it takes time, it has flaws, but it's good. (I did not make it, I'm not associated with them, I actually made a diff app for studying Pimsleur Japanese, will share later). Personally I'm just doing meaning, not on and kun readings. Like I said, speaking is for another "time of study".
The second is an old copy of Read Japanese Today. It uses your Neural Networks and teaches you all 300 base Kanji. From the pictoral origin to the current form, and how it becomes Kanji you already know. This forms neural networks similar to Heisig's Remembering The Kanji (which I haven't read). Honestly, I find 300 much less intimidating (now 400 in the current edition) than all 2000 Joyo Kanji. But with those 300, you can "piece together" the other symbols. Suddenly you're reading "Doubutsuen" and know exactly what everything means, even no Japanese knowledge and you'll say "Oh, zoo". I found a similar book at the library, but it didn't form the same neural networks and was hard to read. It had "From their ancestral origin" in the title. Amazon has no reviews on it, but Read Japanese Today has many, good sign.
Like the post above, get the meaning down. Read Japanese Today luckily gives you the meaning, the readings, why Kanji changes from compounds to single readings, and gives that "Aha!" to Japanese sentence structure that no other text has given me.
Second-Last, Journal! Write Write Write! Thanks to the above books, I believe I don't need a pen anymore, but I do need to use IME and type my day out in Word or something, then visually see the kanji be used. This gives you interaction. If it's not working for memory, then find the stroke order and write it. If you know Kana, then you know stroke order matters. Literally, meanings change if you write differently sometimes.
Lastly, practice. I'm here at JapanesePod because I feel like the structure is near Pimsleur in Quality. The memorization, speaking, listening, and repetition within conversation nearly matches Pimsleur, and I still remember my Russian from 5 years ago. Not my college russian, but my pimsleur Russian. (All like, 20 words, but I sepak and understand them well enough to trick natives into thinking I'm from Russia). So this is a great compliment for JapanesePod101. Why bother writing it down if you can't say it out loud?
As you can tell, I'm lazy. I get as much results as I can in as minimal time as possible. I'm preparing for a trip to Japan, and I want to be able to catch the train. I noticed there were no apps for listening to Pimsleur before bed, as iTunes makes every audiobook have one impossibly long track hours long. How are you supposed to turn it on and know where you were when you wake up? Some apps came close, but none kept track, so I made one. Unfortunately it doesn't work on podcasts yet, and I don't feel like spamming my own stuff without JapanesePod's permission.
Luckily their lessons aren't hours long, you really don't need it. But I made it so I could study Japanese. I just work as a dev so I can't devote all my time to that stuff.