Here's mine (in no particular order):
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Animal Crossing: New Leaf - My most played 3DS game, and in my opinion the best in the series so far.
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Etrian Odyssey IV: Legends of the Titan - Even though I haven't finished it yet, I've had a lot of fun with it.
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Fantasy Life - An awesome game that's even better with friends.
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Fire Emblem: Awakening -A great entry in the series, even if nobody has feet.
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Rune Factory 4 - Lots of gameplay that will keep you busy for a long while.
While we're on the topic, why not also list our favorite download-only 3DS titles? (virtual console games don't count)
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Azure Striker Gunvolt - An awesome but short game that plays similarly to
Mega Man Zero series.
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Liberation Maiden - Another short but fun game.
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Gunman Clive - Very cheap, and very worth the price it costs.
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Senran Kagura Burst - It's a pretty decent fast-paced beat em up, though if you can't get past the... fanservice... I'd advise avoiding it.
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Flipnote Studio 3D - Not really a game, but it's a pretty nifty application. Making flipnotes is fun.