I didnt play a lot of 3DS but:
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Monster Hunter 3U (my fave)
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Monster Hunter Generations (Only one on my list I havent personally played)
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Fire Emblem Awakening
More importantly, DS:
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Castlevania Order of Ecclesia (if you only play one this is it)
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Castlevania Dawn of Sorrow (not fond of Portrait of Ruin)
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The World Ends With You
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Bowsers Inside Story
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Advance Wars: Dual Strike (best in the series)
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GTA Chinatown Wars (only gta title I got into, loved the top down view and drug selling system)
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Rhythm Heaven
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Dragon Quest V: Hand of the Heavenly Bride (Best JRPG and one of the few that managed to keep me hooked)
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Mario & Luigi: Partners in Time
Damn, after writing out these games, I want to really try to get an Emulator on Steam Deck working and play me some DQV or Mario & Luigi.