Nintendo's main franchises take the fourth and third spots.
#4 - The Legend of Zelda: The Minish Cap
Perhaps the last great 2D Zelda game, Minish Cap is one of the most unique entries in the series. The "dual-world" mechanic comes through Link's ability to grow and shrink thanks to his adorable living hat (of the title). Once the size of a pea, Link can find and communicate with a miniature race of mouse-like people called the Minish. In the larger world, Link does the typical Zelda thing--running from dungeon to dungeon and collecting new and interesting items (including the memorable Gust Jar).
The game also involves a larger meta-game. Link collects bits called Kinstones and attempts to find NPC's with matching stones to gain special items and prizes. It's an excellent game that every Zelda fan should play, especially those who like Link to the Past and Link's Awakening. Check out our review here.
#3 - Mario & Luigi: Superstar Saga

Here at NWR, we love the Mario & Luigi games, but that first GBA game has a special place in our hearts. The player controls our boys together in this incredibly well-written, well-paced, action-packed RPG that's reminiscent of both the much beloved SNES Super Mario RPG (there's even a cameo from Geno) and the Paper Mario series. The game is superbly animated and features the best battle system in the entire trilogy, with players learning fairly complex button sequences to deal incredible damage to enemies and bosses. And of course, Mario & Luigi gave the world the joy that is Fawful, one of the best antagonists in any Mario series. Read our review for more details.