The way that works best for me, personally, is using the link method to remember Japanese characters (works well for Hiragana, Katakana and Kanji).
Writing them all out a couple of times first helps me to remember the stroke order (knowing how they're written helps you remember them better). Then I pick something familiar that the character reminds me of, or something it looks or sounds like, and it helps me remember them. This works well with some of the kanji which are pictographs, so the character looks like what they represent anyway.
Also, using flash cards regularly helps to remember them long term. This works for vocabulary as well as learning the characters.
Repeating these two things together work pretty well for me, as long as I review them regularly, and keep revising old ones so you don't forget them. Eventually you will need to revise the older ones less and less often.
Hope this helps :)