
I didn't have the Zapper for my NES, but I did enjoy playing Duck Hunt at a friend's house as a kid. I liked how you could use a 2nd controller to move the ducks around!
There are a lot of Hogan's Alley mini-games in the Wario Ware series.
My favorite light gun games are the Point Blank titles by Namco. I wish Namco would revisit Point Blank, but I guess it's harder to do light gun games on today's TVs.