I think my number one would be Dragon Quest V. I really love a good coming of age story, and it hits in so many ways that make you want to keep going and see your journey through. There are really good plot points, the game does some great story telling through its own gameplay mechanics, and even the subplots are fun mini-adventures. It's got a really lovable cast and has the ability to turn some characters you might hate at first into rather redeemable people.
Lisa the Painful is another really fantastic one. I think the DLC added was sort of unneeded and sloppier in writing compared to the base game, but ignoring that, the game is incredible. It gets compared to Earthbound, which is sort of fair, but it's own different beast. You're in a post-apocalyptic world where there's no women, there are bizarre monsters, the currency is dirty magazines, and everything is in shambles, but it's somehow one of the most interesting worlds I've seen. I think the writing is really to the game's credit, because at one moment, the game will make you feel absolutely awful as if nothing matters, and then immediately follow it up with some joke that is incredible to bring you right back to your spirits in the worst ways possible. This game never got the acclaim that Undertale did, and while I think Undertale is fine, I always thought Lisa the Painful to be the much better game. Maybe it's good that this game didn't blow up for people to sort of "ruin" in a sense, but I highly recommend people check it out.
After that, I recently played through Final Fantasy 7, and man, that was a ride. I don't ever plan to look into the side-games, just on that one as its own singular thing, and I thought it was fantastic. I knew the one major plot thing that I think everyone knows by now, but even that still had a bit of an impact on me. Each side character had a relatively interesting backstory too, and Barret, a guy I went in thinking I wouldn't care for ended up being one of my favorites and a mainstay on my team. I don't think I'll have the opportunity to play the RE:make, nor do I think I want to. I kind of like this insular journey I had, and it had me wanting to know what was going to happen next the entire time.
Majora's Mask is also up there. I don't think I have to sing its praises too much, because it's been done so many times on this site, but it's good. A somber trip down apocalypse-lane, and you feel a weight on your shoulders in the best way. Every joyful event in the story is bittersweet knowing that you'll likely reverse it so you can carry on your journey, but that's sort of life (not literally, but the fleeting feeling of happiness).
I could keep going, but I think the final game I'd like to mention is the original Chibi Robo on Gamecube. It starts out as a sort of wacky experience about being pint-sized in the world of the average home, but it tackles some interesting themes like problems within home life, death, and what it's like from different and rather unique perspectives. It has such a unique air on how it's set-up, and it's fun to be part of this weird adventure. A single house feels like enough for an entire game's location, and it's a shame that I don't think we'll ever get a proper sequel that the series deserves.