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Being an IT guy and a student of Japanese, I'm expectedly a fan of using software to study.  I've tried just about every type of Japanese learning software there is, so here I've compiled a list of my favorites:

The Rosetta Stone (PC / Mac) - www.rosettastone.com
The Rosetta Stone is the Ferrari of language learning software.  It's fun and extremely interactive, engaging all the senses to maximize retention.  It's automatic lesson review feature quizzes like a real teacher, and it's the only software I've ever found that supports voice recognition, making speaking practice possible.  It's by far the software that comes closest to classroom learning.

* Impeccably designed to engage all the senses
* Supports voice recognition
* Intelligent review feature maximizes retention
* Available for Mac

* Expensive
* Does not support kanji text input
* Not for very advanced learners--it's getting a little easy for me

King Kanji (Windows Mobile) - www.gakusoft.com
Nothing beats a good ol' PDA (or smartphone) with a stylus for studying kanji.  I tried to switch to an iPhone platform, but using my finger to write just wasn't natural and wasn't comfortable.  I even tried an iPhone stylus, but it didn't work well because the iPhone is designed for a finger.  King Kanji is a clean and effectively-designed software that simply asks you to write a kanji for a given meaning / pronunciation.  It will give colorful feedback on your stroke order as you write and will provide stroke animation if/when you need it.  Keep cycling through the lesson, and you'll eventually get it!

* Simple, but effective kanji study tool
* Lots of included lessons
* Well worth the money
* Great for on-the-train studying

* Sometimes I wish the included lessons were a bit shorter or there were an option to break the lesson into parts
* Some lessons contain kanji study notes, but an option to enter my own study notes would be nice

Stackz (PC / Windows Mobile) - www.stackz.com
The perfect companion for kanji study software is vocabulary study software.  Stackz is a general purpose flashcard program with an intuitive interface and powerful customization options.  As I learn new Japanese vocabulary, I enter it into a 4-column spreadsheet (kanji, kana, English meaning, and notes).  Stackz allows me to take these spreadsheets I make and create flashcards.  Supporting study notes on the flashcards is an extremely useful option since my own mnemonic devices are often the key to remembering new vocabulary.

* Supports adding study notes to flashcards
* Versatile--can be used to study anything
* Many free, downloadable lessons
* Great for on-the-train studying

* A Mac version would be nice

Read the Kanji (website) - www.readthekanji.com
I'll be honest and say that I'm not a big fan of kanji flashcards because I personally remember kanji better by writing it.  If you can write it, you can read it; but the reverse is not true (unless you're using a computer).  Nevertheless, the website www.readthekanji.com is well worth mentioning.  It's a kanji flashcard system that seeks to address the tedium and retention issues encountered in standard kanji flashcard approaches.  It attacks your weaknesses with an intelligent tracking and review mechanism that adjusts to your level.

* Free trial
* $10 for a lifetime membership
* Being a website, it's cross-platform

* Being a website, it requires Internet access
* I think it used to be free

Japanese Flip (iOS)
Japanese Flip is a very simple flashcard program great for lazy students like me.  Its lessons are broken down into the JLPT levels, and it intelligently tracks your knowledge by noting how often you miss words.  It has a very clean interface and it's great for on-the-go learning.

* Great price
* Pre-made lesson structure based on JLPT levels is great for students too lazy to create their own lessons
* iPhone platform is the ultimate in portable learning

* Does not support adding custom study notes to the flashcards

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