Kanji are the bane of my existence. Like most learners of Japanese, I have trouble making them stick. I don't feel too bad about it because even native speakers don't exactly love kanji-- most literate adults only know about 2,000 of 6,000 or so that exist and there are a variety of gameshows that revolve around giving the correct reading of various obscure ones.
In my never-ending effort to increase my Kanji retention, I stumbled across Declan Software's site.
I've been using their ReadWrite Kanji program for about 5 months now and have found it to be insanely useful. The basic package contains 1945 kanji (the Jouyou kanji until November of last year) which is enough to become functionally literate.
It has information on everything from the expected-- on & kun readings, stroke order, pronunciation quizes-- to the unexpected, but welcome-- radical identification and a kanji seek-n-find type exercises. They also offer programs that teach hiragana (above) and katakana, as well as a Japanese dictionary and flashcard program. Versions are also available for Windows Mobile / Pocket PC, and the flashcard program is available for iPhone/iPad.
You can download a trial version of the program for free. But lifetime registration is a scant $12.80, making this one of the first freeware programs I've ever paid to register.