The Legend of Zelda: A link to the Past.
At the time, and having played the original two, A link to the Past was such a massive step up in the genre, that no other game came close for years. In fact, many games were made to look extremely similar. Perhaps it was due to system limitations, I don't know - but Secret of Mana was a prime example of how the entire genre had been transformed by the former. And, of course, the latter was developed by the same people responsible for other classics within the genre, such as some of the Final Fantasy games.
Looking at the game, it represented a continuum, characters within a fantasy world that was the same yet ever expanding. Further, the basis of the story was classic enough that everyone could relate to the Repunzel like setting but yet with a good mix of memorable, unique characters who all had a story of their own. Interestingly, I still remember owning the Nintendo hand-held gaming devices that included the princess who needed rescuing from the tyrant, who at the time was surprisingly called Donkey Kong.
To this day, I still remember discussing the game with someone older. During the conversation, he mentioned finding the game vague. Of course, that made little sense to me at the time, not just because he was using a difficult word that I simply did not understand but because games at that time were still made to represent stories that evolved from books and required a certain amount of imagination.
Ominously, perhaps it was a sign of what is to come.
On a different note, the two quotes below are for emphasis. And although I only started playing the Homeworld series from the second part, the same still applies for me.
Homeworld. Great story, beautiful graphics, the best atmosphere of any game I've played, excellent choice of music and unique gameplay. I really hope they release a third.
mario kart, the most fun you can have with your pants on