Interesting picks--I've played through FFV but only about a quarter of the way through FE:A.
My all-time favs are Final Fantasy VII, Final Fantasy VI, and Chrono Trigger.
Yeah I know it's entirely too mainstream, but what can I say? ;-)
I recently played through Earthbound (finally!). In a lot of ways the gameplay is pretty antiquated, but overall it's one of the finest pieces of art I've ever seen.