My favorite RPG overall is Final Fantasy VII, though if it was the original alone, that wouldn't hold true. I love the movie, the sequel and the fandom (yes the wonderfully creative and active fandom) more than the original game by itself. What makes it my favorite it a combination of all of that. My liking for Reno and Sephiroth helps too.
In terms of game play my favorite is the action RPG Phantasy Star Portable 2, all it needs is the ability to jump (as in really jump, not kind of jump then roll) and it would be as close as it gets to perfect. I really like being able to jump despite my favorite type of games being ARPGs and RPGs, which don't always have jumps. This game doesn't have the memorable story of FFVII, it's good, but not quite up there, I'm just talking about the game play itself here. It has the option to play online with other people so that helps.
As for the game that would stand as my favorite on its own, not relying on sequels (as I think of the sequel as just okay, and not on favs list), and not relying on the fun times with the fandom, which is relatively quiet by now, at least in comparison to others... Chorono Trigger. It has characters that I really like, my favorites being Magus and Lucca, but it's not just a liking for the characters that makes me like the game. It caught my attention right from the start and I never got bored. I loved how it integrated the time travel elements to the plot. Beautiful graphics, awesome story line, fun battles. It stands strongly on its own in every aspect and even if it had no fandom or sequel, or rather despite it having an okay sequel rather than a grand one (IMO), it would still continue to be right up there in my favorites list...
To summarize, taking all the aspects of the games with the games themselves, overall my favorites list goes like this:
Final Fantasy VII - the game that got me into the FF series as before that I didn't get what the FF hype was about, good times with the fandom (fics, art, role play ect.), awesome character designs and development.
Chrono Trigger - my fav on its own, though it gets bumped into 2nd of I include Advent Children and Crisis Core together. Awesome plot, characters and gameplay.
Super Mario RPG: Legend of the Seven Stars - this was my first RPG and what got me into RPGs back when I knew nothing about them. The story is full of awesome amusing moments. It's a beautiful game, has great music and it has my favorite Mario character: Boshi. The only thing it needed to be my perfect Mario game is my second fav character and #1 koopaling, Ludwig. Being able to take Yoshi (and Boshi!) out of Yo'ster Isle would have been awesome too.
Phantasy Star IV - I like the ARPG style of the new Phantasy Star Universe, but plot-wise, PSIV: End of the Millennium is still my third favorite.
The 5th spot changes far too often as there are many other games I like that are constantly fighting for it. Valkyrie Profile: Lenneth, Phantasy Star Portable 2 and several others are among them.
Granted I might have become harder to impress during the years, but not because I'm pickier. I'm less picky now that most games look pretty, which was what got me into RPGs in the first place when they were known as having the best graphics. I'm willing to give more games a chance, but because they all meet my graphics standards by now, but they won't get as many bonus points for being pretty. Maybe that's why it's more difficult for newer games to stand out, they need a stronger story since I have more to choose from.
I really like Unchained Blades in terms of story, though the battle style isn't my favorite, it's still good and not overly grindy. Even so, awesome characters aside, the reply value isn't up there, albeit it does really make me wish there was an anime for it. It's a bit predictable in some parts, but in the most charming and amusing way.