#3 Freespace 2
Freespace 2 is a masterpiece, plain and simple. It's the best game in its genre, even 17 years after its original release in 1999. Not a single other game of its kind has ever featured such masterful mission structuring, where events often unfold in surprising, yet always logical ways. The gameplay has a lot of depth, while being simple enough to learn that everyone can easily play the game. The fact that there is a strong community still surrounding the game speaks volumes about its quality. Fans have kept Freespace 2 alive for nearly two decades, updating its graphics and even creating their own games based on its engine. Freespace 2 is such a great game in my opinion that it will likely never fall out of my top three.
Hint for my #2:
A JRPG that has attained cult status over the years since its release. Many fans, including me, still hope that someday it will get a sequel on a modern console. There's at least one person here who knows exactly what game I am talking about.