Another option since OCR isn't really viable for this stuff is to use a handwriting engine. It's especially handy for transcribing kanji.
If you happen to be using Windows every version since XP has had the tablet PC input panel, and in lieu of an actual tablet you can use the mouse to write instead. For setup, you would go into keyboard/input settings and toggle on Japanese input support from the (long) list. When the input panel is open you select a window for a target that uses text, select the language from the list, and draw. Works best when you know the stroke order, and if you get close the toggle up above gives a list of what it thinks you were close to. Hit enter or click away from the dialog to copy the text into whatever window it was targeting. It works significantly better than Google's handwriting input (relying in large part on OCR), mostly because of the addition of stroke comparison.