When I read a digital manga or VN, I take a screenshot and add it to a dictionary word list. Then I also add it to a physical word list in a notebook (partly because I love Japanese penmanship and this is a quick way to practice). Finally I go through the word list and find which words I want to review on Anki, which I make completely manually with zero automation (so I also end up practicing Japanese typing).
Between the initial encounter when reading, adding to a digital and physical word list, and typing out cards, that is four chances to familiarize myself with every new word I bother to mine before I let Anki deal with the rest.
It might or mightn't be placebo, but the words for which I do this whole song and dance feels like they stick much faster than words that don't get the same treatment, like words I pick up from a vocab list for the sake of knowledge gap fillers. I just go straight to making cards for those as I see them.
This probably takes me about an hour and a half give or take, including an hour of reading and a half hour of actual card preparation. Luckily for me, I got past the stage of needing to spare time for textbook study years ago, and this process is my only "official" structured study time. I might spend much more than an hour and a half on Japanese per day, but I don't count media consumption as study time if I don't purposefully make an effort to remember unknown words.
It gets a bit tedious at times, but… What can I say? I enjoy the process. On a slightly unrelated note, having a nice fountain pen and mechanical keyboard to play with makes the whole thing more fun, though that's neither here nor there, necessarily.
by ignoremesenpie