Not really a big fan of themes but I've got a few like Majora's Mask theme in my Majora's Mask 3DS XL (my main) then Pikmin 3, and the free Gurumin theme I got when I bought the game. My Fire Emblem XL also has this Dragon Quest VII theme I got from buying the game digitally.
I started using the Hello Kitty Crystal Princess theme over the winter because I loved the colours and snow. The only other theme I have is the purple lace Espeon and Umbreon one, which I used for a very long time.
It depends on the faceplates. If I use the Mario plates, I use the Mario theme. If I use the Splatoon plates, I use the Splatoon theme. If I use the Majora's Mask plates, I use the Dire Moon theme. If I use the Monado plates, I use the Monado theme. I also use matching badges from the arcade to label folders and replace the icons.
On my New 3DS XL HHD version, I use the HHD-Office theme, obviously, as well as Animal Crossing badges.
I'm currently rocking the Majoras Mask theme. I don't even particularly care for Majoras Mask all that much, but I love the color scheme and the sound effects/music are to die for.
Wish I could get an Ocarina of Time theme that is of the same quality.
Mine is currently the Team Rocket one because it plays the Rocket Hideout music and sounds awesome. I would probably buy more themes if they had better music on them. Like why would Shadow the Hedgehog's theme play Radical Highway instead of Shadow's theme? And a cool Eevee them plays dream suite or global link music I think. I would have got them if the music wasn't so disappointing.