Vagrant Story, and Xenogears.
Gameplay wise, I'd say they are the best.
Eh, I'd disagree... Ambitious and interesting, yes, but both have some annoying flaws. VS becomes menu hell, the mechanics are not clear (even the in game manual has mistakes), and it's possible even the devs didn't fully understand what they had programmed O_o Xenogears I don't have as many gripes, and it has been awhile, but I recall a few points where I was confused about abilities or something...
Valkyrie Profile and Star Ocean: The Second Story
I REALLY need to find time to play those >_<
WA2 I would definitely put up there. Puzzle solving is fun, like you said, very Zelda. And on top of that, the combat mechanics are fun imo: nothing groundbreaking, but enough to set it apart.
Final Fantasy V. Even though the playstation port's kind of meh, it's still Final Fantasy V.
Huh, what problems were there with the 5 port from anthology? I was under the impression that port was generally fine. I know chronicles butchered chrono trigger.
I am compelled to give my vote to
FF tactics >_< y'all know it's my favorite FF: I think it is the best incarnation of a job system, being able to freely recruit generics and build your party how you want is awesome! So much depth and freedom! I know srpg's are not for everyone though and battles can take awhile, but I cannot help myself >_< Also Agrais