I play Yahtzee on the computer often and that's how they play, with the bonus Yahtzee being applied everywhere. When I first started playing the game, there was an actual box for Bonus Yahtzees and you would just add to it if you got one, but you still had to complete the other boxes. I think I prefer that way, because a bonus yahtzee is not the same thing as a Large straight, for example.
My favorite board game is Stratego. Occasionally I'll introduce house rules where bombs can move, where the spy can take out any piece as long as he strikes first, where some scouts (renamed SEALs) can cross water, etc.
Growing up I thought that was how Monopoly was suppose to be played. Didn't learn until high school that it was a "house" rule that somehow passed down to everyone I knew that played the game. A friend and I once played the game an entire day. We finally had to quit and accept the fact that allowing each other unlimited credit meant the game would never end.
We play Yahtzee for money all the time at the bars and we always play that you get the 100 point bonus for extra Yahtzees. We usually play for $.25 a point. It doesn't sound like a lot but it can add up. I once lost $346 in one game.