A daunting part of learning Japanese is memorising reams and reams of words. Sitting down and forcing endless amounts of un-contextualised information into your brain is hard. Ideally, of course, you would learn in-situ. For a lot of people that isn't possible.
- Before You Know It.
Basically just a simple program which asks you to memorise and then type words in your language and then the foreign language. Also supports sound, lets you make as many lists as you like and has a nice selection of hands to turn your cards for you.
It's 50USD to buy, but the free version has a wide and great selection of vocab to get you started. The price-tag is a bit steep when compared to the following free alternatives.
No longer free but still excellent site very similar to Before You Know It. Has loads of custom made lists to cover all major tests, as well as specific themes. Like BYKi it supports dozens of other languages too. Also has a couple of famous voice actors reading the words and sentences.
Spaced Repitition System. Smart.fm runs on this idea.
The program will show viewed vocab at timed intervals spaced by some mathematical formula to best help you remember them. The most popular one of these is Anki. Not much to look at, but useful. This is apparently scientifically proven to be the most effective method, providing you stick with it long-term.
The best thing about these three is that they save your progress. They also allow you to isolate your weaknesses. All three are also available on portable tools such as phones or iPods.
Of the three I think the first two are the best, mainly because they ask you to type your answers. This is an effective way of memorising the vocab, spelling and appearance of the target language, and interacting with your flashcards (as opposed to just shuffling them) is a high priority.
But beware, characters in anime and manga often use words/phrases in ways which normal people do not, so exercise caution when talking to Japanese friends or you may sound like a moe.