Eugh, truth be told, I stopped knowing what my favorite game series was years ago. I used to be very passionate about the
Legend of Zelda, and I mean, I still am, but I'm not sure if I could consider it my favorite anymore. Even so,
A Link to the Past is still probably amongst my all-time favorite games.
Like
@Moogi Beans,
Harvest Moon Story of Seasons and
Rune Factory are probably up there somewhere. I haven't actually played
Story of Seasons--that's their new series name since Natsume stole the rights to "Harvest Moon" and make their own games now. All of the newer installments; I think the 3DS ones especially, all seem generally the same in both story and mechanics. They don't really offer anything new to the series, so I'm probably not missing much. In hindsight,
Harvest Moon DS is probably my favorite. As far as
Rune Factory goes, my favorite is the first one.