The Pallet Town theme from FR/LG is very nostalgic since Pokemon LeafGreen was my first Pokemon game
I love The Minish Woods theme and it is also nostalgic, child me was lost in the Minish Woods forever, I was very excited when I found Ezlo, and I love the Minish Cap so much mainly due to nostalgic reasons too
The Rainbow Route theme from Kirby and the Amazing Mirror, I'm not a big fan of Kirby but I love the Amazing Mirror, I think it was my first nintendo game ever, I used to spend the entire day playing Kirby, until I got Pokemon
Although it's not a theme, but the Hamha! Sound effect from the Hamtaro games really brings back some happy memories
All of these nostalgic themes are from GBA games cuz it was my first console ever.