It really hurts not to give it to XD: Gale of Darkness for the sake of nostalgia, but it has to go to the first Mystery Dungeon for me. So many great memories playing it, and I was beyond pumped when the remake came out. The ending of the main story is also the first time I remember a video game straight up making me cry, so definitely a deep emotional connection there.
Also an honorable for Pokemon Ranger. Really wish they could have given it a remake as well, but I suppose they would also have to retool the capture mechanics big time.