Every single word encountered this way should make its way into your SRS after learning it.
As far as deck strategies, I was an Anki user and didn't like getting too many decks going at once. I tried doing separate decks for each book, video game, etc I was working my way through but it turned out to be huge pain. Now I favor only one deck per language for recognition, one for writing and one for ear training.
The problem with shared decks is that Anki is not a very good way of learning information for the very first time. Seeing the material from another source, like a textbook or encountering it in the wild and then studying by tags is the process I find to be the best flow for me. I have a cram deck for all the vocabulary I have ever studied, one for the current chapter I'm studying, and if I'm taking a class one for all the vocabulary I've studied in the class that semester or year. With textbooks, I read over the vocabulary and tag words or add an example sentence if I need to but I often don't have to. Using this method I can learn somewhere between 50-100 new words in a week if I need to with pretty good recall.
However I have another cram deck that is tagged with words that are the top 2000 and 6000 most common. Unless I have seen the word previously I find even going through 10 words to be a painful process and it takes me much longer to memorize. I have that cram deck setup to only show me 5 new words a day and mostly use it as a review deck.
Edit: Grammar
Personally, now, I am concentrating on Anki, and I build my stacks by adding words and short phrases as I come across them during the day. It is an excellent, if clunky, tool: it allows you to add TeX for learning equations, etc; its model lets you define different types of data structure ('Note'), from which you can define different question-responses to learn ('Cards'). The main problem is the limitations of the iOS app, which doesn't let you add new Notes or process your TeX for you.
-[1] EPWING2Anki creates flashcards from a wordlist and a dictionary in EPWING format
-[2] Sub2srs creates flashcards based on a movie and subtitle files
It's also possible to use e.g. spreadsheets to mass-create cards. Further tools analyze e.g. a selection of ebooks and create word frequency lists of unknown words, Combined those tools have greatly assisted my progress.
Also, in my comprehension of Japanese on the internet, a firefox extension rikai-chan or the chrome version rikai-kun (which I use) is invaluable. With computers even Japanese people don't need to know how to write kanji, they just type the hiragana and hit space til they see it. This extension allows you to highlight the kanji, going in the other direction (kanji -> pronunciation/meaning, use your japanese keyboard to go from pronunciation/hiragana -> kanji with spacebar).
Also, for a dictionary I use Alc [2] which I found is very commonly used by Japanese people that need to find English words. The main benefit to using this is that there are many examples of the words used in context, and showing other kanji used for those same meanings. This allows you to make sure the kanji you found for the meaning you want is actually used in, or find the correct kanji for, the context you are trying to use it in. It is important to have a database maintained by people that know proper Japanese for sure, it's much easier to understand broken English than to try to use broken Japanese.
[1] http://www.tofugu.com/resources/wanikani/ [2] http://www.alc.co.jp
Source is here: http://github.com/gojp
Take a look if you have time, feature requests are very welcome :)
Do you mean that on jisho you always use the Japanese search box?
Some of these are copies of other's decks. The vim one is good, even as someone who's normally the vim expert in a given group of Unix bods I still find myself learning.
The git one is crap, I will redo that myself when I get a chance.
The idea / pycharm ones are just a dump of the keybindings. Same for the GitHub one. Its pretty easy to make simple decks.
There's an excellent multimedia deck called "knots" which predictably enough teaches knot tying. Worth a look to see what's possible with Anki.