I think i replied to a thread similar to this quite some time ago, but seeing as it's been a while i shall enlighten you all on my favorite handheld title.
The Legend of Zelda: Link's Awakening was my favorite for many reasons. Although i haven't had the chance to enjoy it in all it's glory on the original gameboy, i did have the chance to play it on my computer. I know pirating is bad, but i cannot play my GBC version. back on topic, the controls were what i expected and nothing special IMO. The gameplay kept me involved in the game, it was fun rapidly pressing A to swing link's sword. The story was very suspenseful and had a screwed up ending, but it grew on me. Link's Awakening was my first handheld Zelda game so it holds a special place in my heart.