Final Fantasy VII's storyline was phenomenal. I loved the progression of that game from beginning to end, especially the City of the Ancients. That music, ooooooooooh my god! I also really liked how the game had a variety of styles a player could take to beat it. I actually played through it once utilizing everything the game had to offer, then I played through again using only one party member (Cloud), with NO materia, and ONLY the starting equipment. It makes for a much more challenging game experience!
Then of course there's the whole "three-party-members-with-hp/mp swap/Quad Magic/Mimic/Knights of the Round materia-instant-death" combo; just cast KOTR with one character, mimic him with the other two, then go make yourself some pasta. It's a 1.5-minute cast time, and they're casting it 12 times
The only games that compare to it in terms of timelessness are Legend of Zelda: A Link to the Past and Chrono Trigger.
I really hope FFXIII delivers, particular the Versus Noctis edition. I really liked the more seedy, gothic nature of FFVII and it looks like they're returning to that with Noctis.