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.
Positive
Impeccably designed to engage all the senses
Supports voice recognition
Intelligent review feature maximizes retention
Available for Mac
Negative
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!
Positive
Simple, but effective kanji study tool
Lots of included lessons
Well worth the money
Great for on-the-train studying
Negative
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.
Positive
Supports adding study notes to flashcards
Versatile--can be used to study anything
Many free, downloadable lessons
Great for on-the-train studying
Negative
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.
Positive
Free trial
$10 for a lifetime membership
Being a website, it's cross-platform
Negative
Being a website, it requires Internet access
I think it used to be free
Japanese Flip (iPod Touch / iPhone) - www.japaneseflip.com
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.
Positive
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
Negative
Does not support adding custom study notes to the flashcards
Japan 
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