You can use Mecab, but I'm not sure if that's going to render on most video players.
If you want to improve your kanji skills though, putting furigana in probably isn't the best way to go. You can hear the pronunciation and see the kanji - you can connect them like that. Otherwise there's a fairly good chance you'll just ignore the kanji and read the furigana.

The answer is pretty much no. None of the subtitle renders support ruby text. As a subtitler if you want to display furigana with Japanese text, you gotta do each ruby as it's own subtitle line, with exact placement on the screen. It's pretty much a nightmare.

I don't know if you mind flash cards, but your probably better off with subs2srs and using Anki's Japanese plugin to generate readings. It won't be 100% correct, but a good majority of what it generates will be spot on.

Can you add them in hiragana in parentheses?  Doing something like 天秤（てんびん） is standard on the Internet and in some video games; I think as HTML5's ruby tag gains wider support and people start using it, this will decrease.  But for now it's pretty common.