Wow... the best... I think every one would agree there are so many good ones its hard to narrow it down, more info would be nice such as what ones you have played so people know what not to list.
A few good ones are
Chrono Trigger
Dragon quest monster, V, IX, Monster
Final Fantasy IV
Nostalgia
Id like to say Pokemon but its story has always been kinda meh, still a great game though. Super Robot Taisen OG Saga Endless Frontier was good. Though might not be the type of turn base you want....
All in all I say go with Chrono trigger.. that game is old but still holding its own even now, And the Ds one has even more stuff for you to do as well.
If you've played that than next id say probably Nostalgia its like final fantasy but you get to actually fight with your air ship
If you've played That I suggest One of the dragon quests you can't really go wrong picking one, though IV is kinda meh.
Those are just my top choices there are many more to choose from...