Phantasy Star gets my vote which, from looking at this thread, is quite the underrated series indeed. PSII and PSIV rival anything the FF series has done. People that thought Aeris dying in FFVII was a big deal clearly never played PSII.

The Dark Cloud series is also a notable mention. I noticed both Phantasy Star and Dark Cloud weren't included in that poll. Quite the error you made there Crossblades.