100 Missiles In Afterburner:
When playing Afterburner, get to the third level and press Left+X. You missile count will go up to 100.

The Bad Ending:
Like Shenmue, Shenmue II has a bad ending if you take too long to beat the game. To see it in this game you need to play until June 31, 1987 in the game and then it will happen when Ryo goes to bed. The quickest way to do this if you want to see it is to play until the Zhangyu Barber's QTE and keep failing it. That way you can get to that date quickly. I won't spoil the bad ending for you but it's pretty cool to watch.