Not in any order, and I can't narrow it down to just 3, but here are some of my favorites, both recent and from when I was a kid:
GBA:
Pokemon Emerald: I had both Ruby and Sapphire as a kid, but I loved the new features like the Battle Frontier.
Hamtaro: Ham-Ham Heartbreak: SUCH a cute game. I've replayed it at least 3 times since I first played it when I was like 7, lol. Brings back memories.
Harvest Moon: More Friends of Mineral Town: My favorite Harvest Moon game. I really liked the music and characters.
NDS:
Ace Attorney Series: Yeah, don't ask me to pick just one. I love this series to death. The characters, the music, the story, the gameplay... EVERYTHING.
Animal Crossing: Wild World The music is my favorite thing about AC:WW. My brother had introduced me to this game when I was pretty young, so this one holds a lot of memories for me, even though I'm pretty sure I just derped around most of the time.
GC:
Tales of Symphonia: Everything. I just...omg. bae. The characters, story, music. I can't express in words how much I love this game lol. Again, I used to watch my brother play it as a kid, and so I came back to it recently and I realized just how great the story is.
3DS:
Animal Crossing: New Leaf: Don't think this needs any explaining, lol. I miss WW's music, but this game is so much more fun.
Pokemon X: I loved the customizable outfits and the new towns and other stuff. I have Alpha Sapphire too, but it feels lackluster compared to X and Y.
PC:
Minecraft: So fun. I've been playing this game for a long time, whenever my friends play and invite me to, lol. There's really so much you can do in it, and I love building things! Never gets old for me. P.S. I've been playing on Jubs's server with a few other people, like Dark, Thunder, Lockfancy, and Caitlin, which more people should totally join! There's a thread for it here in the Gamers' Lounge~