I guess this eventually became popular after lots of ports to other platforms. I always felt bad that I bought it used, but I really didn't know anything about it and had no idea how much I'd end up liking it.
R-Type Final
I never unlocked all the ships, but I sure played the game a lot. Highlights that come to mind include seeing debris from ships falling on traffic far below and a stage with 5-6 different versions ranging from desert to underwater.
Fatal Frame 1, 2, and 3
The first one is still the scariest video game I've ever played. I don't know what it is about this series, but as much as I like the games I can never seem to finish one. I got pretty far in all three, but always got stuck, lost, or distracted.
Baldur's Gate: Dark Alliance
All of the 3D Gauntlet games were awful, in my opinion, but fortunately Dark Alliance gave us a worthy successor to that series. I'd hoped Diablo 3 would be as good as this game (and its sequel), but no such luck. Or maybe it was just too similar and didn't seem to offer anything new.
Rez
While technically a Dreamcast game, I never had a Dreamcast so I was happy to see it ported to PS2. I don't know that there's much left to say about the game at this point, though I'm trying to figure out whether the PS4 port has slightly enhanced music or whether my sound system is just better now.
Gradius V
Already mentioned, but one of my favorites. I never could beat the game, though. I always lost too many lives on the asteroid stage to get much farther.
Growlanser: Generations
As long as you turn off the voices, these are some compelling tactical RPGs. Growlanser 2 is definitely the highlight, but both are worth playing.