Oh, there are so many.
Golden Sun: Dark Dawn is definitely one of them, a Livewire just said. I won't spoil anything, but it was clearly meant to have one. Hopefully it will one day.
I think Pokemon Conquest is befitting of a sequel as well. I was skeptical about the idea when I first heard of it, but as soon as I played the game was more than impressed. I would love to see a sequel to this in some form, or at least another Pokemon tactical RPG.
I would love to see the Final Fantasy VI characters go on another adventure. The ending tied up all the loose bits, but perhaps something could come from a little creative thinking. I consider FFVI to be my personal favorite game of all time, and I'd more than enjoy a sequel, though it seems Square-Enix has forgotten this gem.
Super Princess Peach 2 anyone? Like many veteran gamers I found this game to be too easy. Much too easy. Yet at the same time, I praised the role reversal the game brought, and how they managed to keep Peach right in character even as the protagonist. A sequel with more challenging elements could definitely be done, just as Luigi's Mansion: Dark Moon answered my prayers.