In no specific order:
4 because it's a classic representation of not only an old school RPG, but an FF game as well. It just sticks to you and it really feels like one of those childhood stories you grew up with. You just get a sense of nostalgia from playing it, even for the very first time.
2 had one of my favorite character progression systems and farily simple yet satisfying story. The progression system had a few kinks in it and wasn't perfect, but it's concept was brilliant. Hell I when I first played it I never once abused the system and I beat it, which is a task I bet most people have never accomplished when it comes to playing this game.
6 is the prime example of what an FF game should be with the best story in the numerical games. A great and meaningful cast, and one of my favorite villains in gaming. The story was great and had tons of memorable moments, and never straddled in insane ville like some of the later games.
7 is second to 6 with a great story and villain as well. I liked it for all the reasons I like 6 really, and the game has taken far too much flak of the years due to stupid fans and ignorant haters. The game is overrated yes, but that doesn't stop it from being good and having one of the deepest protagonists and Villain (before AC ruined them) in the franchise.
9 I have not played all the way through, but I am certain I will end up enjoying msot of it seeing as it's a throwback to the originals.
X was hit and miss but enjoyable none the less. The underlying plot and the world was great, and even though it was bogged down with some stupid characters and a few tangents, it still remained enjoyable.
Tactics: War of the Lions hits up there with 6 and 7 as having one of the best stories in the series and it shows. The gameplay is unparalleled as well with the most perfected job system in the series.
Crisis Core is the only good thing it come out of the FF7 anthology and I loved it. It was a great and very personal game as you followed Zack to his end. It really shined light one an important and yet underplayed character in FF7, and he turned out to be one of the best characters in the franchise.
Dissidia just plain kicks ass. It's fun, it's deep, it's an FF fans wet dream and SE really outdid themselves. One fo the best fighting games I have ever played and it still continues to be fun even a year later of continuous play. Such a unique fighter and even with the FF stuff stripped away, it still manages to be an awesome fighter that stands on it's own without the FF label.
*some FF8 fans quote here, removed name because it doesn't matter*
It's not just the junction system that made people hate the game, it's primarily the terrible story too. It had one of the worst stories in the entire series, let alone in any video game, and compact that with the fairly unintuitive, busy, and needlessly complex junction system and the chore that was drawing. It was just a terrible mess of a game, I felt like going into a murderous rage after completing that story and just beat down whoever wrote that garbage.
