It's really hard to pick just one game, and if I started listing favorites it'd go on forever. The ones that most consistently come to mind are Wario Land 4, Symphony of the Night, and Metal Gear Solid 2. You can tell by the first two I really like pixel art, and MGS 2 did a lot of really neat themes and ideas that work well in the game medium. Usually when people think of 4th wall breaking they look at that goofy psycho mantis fight, but MGS2 did a lot by commenting on game sequels in general and subverting expectations.
Wario Land 4 I love the personality and pacing of, as well as it's sound track (too bad GBA isn't that good at outputting sound). SOTN I think most people know is great already, I love all the options it gives players for how they want to go around the castle and play.
I think I chose these three because of all the games I like, these are the ones that I would like to make something most similar to one day, or at least let influence me the most. I don't think I'm skilled enough for it yet though (maybe for Wario Land 4, but definitely not the others).