FFTA is my all-time favorite, with FFT very high up, but since the "other" category doesn't do them justice, I'll give you my top 5 main games. In chronological order.

FFIV - the most classic FF I can think of. Really, when I think FF, IV just seems to be the one that sums up the series the most. Though it wasn't until the DS remake that I really appreciated this game. I loved how all characters had set jobs that were actually worked into the story, how the party composition rotated along the way. It was just a very nice, cohesive experience with all elements of the game working together to really make something memorable. Also, this is the only main title with a five-member party. Why hasn't this become a more frequent thing?

FFV - I loved the job system SO MUUUUUUCH!!!!!!! Also, I really enjoyed how silly and self-aware the story was. I loved the interactions with the characters, and the multiple worlds. And for all it's silliness, this game had some surprising, hard-hitting story elements. The stakes were really high and some scenes were very emotional, which was really cool.

FFVI - easily the darkest game in the series, as well as one of the most artistically interesting. I loved the mood whiplash with very dark scenes being juxtaposed with some absurd humor elements. While the game was a bit too easy for my taste, it's definitely one of my favorite games of all time for how well it created its atmosphere, how quirky the characters were, and overall for shifting the genre in a direction that made it want to be more than just a video game.

FFIX - I squeed with glee when I played it for the first time. It felt really nice to get a throwback to the old games (not that I didn't enjoy VII and VIII), in so many ways. Four-character parties were a welcome return to the series roots, and while we didn't get a job system this time, the characters are designed in a way that really brings back memories of those games with those classes, and I really enjoyed the point-based ability system as well. The story also nicely juxtaposes vivid, colorful, storybook like visuals, with an actually poignant story about dealing with life and death.

FFXII - this was a revolution in so many ways, and I'm so glad the backlash against this has died down. The combat was one of the most fun I'd had in years, with a really ground-breaking AI system where you got to design all your AI scripts from the ground up. I also loved the exploration of the world, which was huge, if still segmented, but still beautiful and immersive, with tons of lore to keep you captivated. And I really liked the more distanced and subtle take on the story and characters, who really broke the mold of the JRPG formula that had become really annoying and stale at that point. Definitely my favorite numbered game.