Speaking for myself I think Final Fantasy VII is the best of the bunch, perhaps closely followed by X, though X suffers from the fact that the ending (Final Mission) was never released for the US Audience. One of the biggest grudges I hold over gaming.
When it comes to Final Fantasy VII I will say a few things
#1: The game is pretty bloody old, and is technologically dated. One of the reasons why so many people have been desperatly hoping for a remake.
#2: The plotline for the time was revolutionary, a lot of people ramble on about stereotypes, whiny emos, and everything else. Honestly all of those people are universally people jumping on a hater bandwagon and I doubt any of them played the game, especially when it came out like they claim.
See, one of the big secrets of Final Fantasy VII is that when the game came out it *WASN'T* a stereotype. A lot of that stuff was an original take on the fantasy genere, a lot of the themes of Angst and such were not all that popular at the time, and truthfully this game was one of the things that made them popular and helped turn them into a stereotype.
It can be argued that Final Fantasy VII is not a stereotype that was bandwagoning, but rather one of the wellsprings from which the stereotypes derived.
#3: Going into another discussion that took place here before, it is debatable as to whether Cloud was really "Emo". To be brutally honest with you, to begin with Cloud is a cocky, arrogant, jerk. Exactly the opposite of the standard emo personality (weighed more towards the Japanese spikey haired punk stereotype). This is why the bits with him cross dressing at the beginning are funny is because he is hardly an emo girly man. He is also constantly griped at for acting like "Mr. Big Shot former member of Soldier".
Cloud doesn't really go "Emo" until his memories start to come back in force, and that takes a while, and eventually drives him catatonic. The thing is that Cloud starts out as a punk, goes deeply Emo (for a reason), and then eventually gets out of it and comes out and does the hero thing to save the world.
In the extended storyline his experiences (Love Triangle with the death of Aeris, decimation of the world, living a lie) has left him an emotional wreck. The whole "Advent Children" movie is about him getting over it.
#4: Part of what makes Final Fantasy VII so great are the characters, none of which were exactly stereotypical for the time (though they WERE imitated). The only one who is really a stereotype is arguably Barret, but to a Japanese mindset he probably seemed fairly original.
What made the characters cool was the amount of detail about them through the entire game. For example when it came to Tifa there was not only the sequence about her growing up with Cloud, and him hiding from her in shame when he didn't make Soldier, but also the seemingly lingering question of how she got out of the Mako reactor in the past... and that, combined with a sequence in a flashback, proves to be the key to gaining her ultimate move. The whole thing also giving her an amount of depth, and at the same time lending some credibility to her skills as a martial artist given the obvious capabilities of the guy who trained her those many years ago.
#5: I personally think anyone who thinks Aeris was "useless" in a battle party for example (sorry to pick on a specific message) is showing a degree of ignorance that belies ever having played the game. The reason why I say this is because she is easily one of the most overpowered characters in the game, and one of the reasons why the "Resurrect Aeris" schtick was such a big deal for a while was not just the fact that people cared about the character (which is an unusual outcry for a video game character) but also because so many people were using her and had come to rely on her abillities. One of her limit breaks called "Planet Protector" (I think I have the name right) in paticular was utterly broken because it turned the party totally invulerable for a number of rounds (as in literally nothing could hurt you). I don't think I need to really explain the ramifications of this abillity and what it could have potentially meant in some of the optional boss battles. Anyone who played the game, especially in it's prime, is liable to know about this.
#6: Perhaps the closest thing I can present to "undisputable proof" (though there is no such thing) of it being at least the most popular game of the series is the fact that it has spawned so much media and captured so much attention long after it was gone. Action figures are no big deal, but arguably the various statues and such people still churn out (which can go for $200 or more in comic shops) say a lot. Not to mention the fact that it has spawned TWO prequel games, a Sequel Game (Dirge) a sequel movie, and a prequel movie. Not all of which are availible in the US (I do not believe the prequel movie which is called "Last Order" or something like that was ever released, nor was the "Before Crisis" game which takes place before the "Crisis Core" game, in that game you play as The Turks).
What's more when it comes to the quality of the storyline, it is notable that the characters are deep enough to have people want further explorations of their characters, and more media involving them. As odd as it sounds the "evil corperation" from Final Fantasy VII was never really that evil (and indeed Rufus presumably dies trying to set things right despite hating the protaganists), this was eventually made fairly clear in the games in it's own way, but lead to it being explored early on. The Turks in paticular were not only "honorable enemies" but given their relationship with Aeris and the final scene where they walk away, it was pretty clear that they weren't really bad either, they merely worked for, and believed in, the other side until the end. The overall effect as things unfolded was rather powerful, and is what people remember.
With no offense to Terra Bradford, and Final Fantasy VI (which many pump up) that game definatly included some great characters like Celes, but was in the final equasion a lot more straight forward with Kefka and such. In Final Fantasy VII the ongoing plotline turns a lot of the original elements of the story on their head. Going into it, you would not have expected Rufus to basically sacrifice everything trying to save the world since he begins being characterized as a pretty typical "big bad".
Other games have done things like this, but arguably Final Fantasy VII was the one that did it best, and introduced a lot of these elements (and even plot twists) to the world of gaming BEFORE they became stereotypes. If you play FF VII nowadays you'd go "oh wow, I didn't see THAT coming" but that's the thing, when that game came out it wasn't a stereotype and a lot of people didn't see those things coming because it was new.
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Apologies for the rant and anyone I might upset (such as addressing one post with doubt). I also apologize for my "rabid fanboyism". These are my thoughts on Final Fantasy VII and what I think about where it fits into gaming history. I think it innovated a lot more than people give it credit for, and even the things it took from other places it wound up doing better than they had ever been done before.
This is simply MY case for why *I* think Final Fantasy VII is the best of the series.
That said as a totally irrelevent point, while it doesn't make my "best of" list I think XIII is best for the babe factor, and I think XII should be killed with fire (no offense to it's fans) simply because I hate Vaan. While it was a throwback I thought IX was too cutesy, I understand what they were trying to do, but despite at least one truely epic moment I thought say Steiner was just too silly, and Quina was in the "Kill it with fire" catagory. I can deal with cutesy minigames in Final Fantasy, but really I do not think I need a walking excuse for a minigame in my party looking freakish and out of place in a party that is already making me roll my eyes at times. I also think tying the ending to the Stellazio Coins "side quest" was just plain wrong especially given the lack of apparent common sense or indication of where they were going with that. Not as bad as XII but IX is up there with the contenders for weakest of the series (soley in my opinion).
