MMMMMMhhhhhh, for me it's difficult, as there are many Mario games' soundtrack I really like, and there are many Mario-related games I didn't play as well!
Anyway, my favorite per genre:
classic 2D Super Mario: Super Mario World
2D Mario-related platfromers (classic Super Mario series + NSMB series + Yoshi series with babies): Yoshi's Island (Flower Garden, Yoshi's Island theme (the one of the file select screen), the best castle music yet, the incredible final boss theme and much more!)
3D Mario: Super Mario Galaxy (honorable mentions: Starship Mario, Puzzle Plank Galaxy and Yoshi Star Galaxy from SMG2, Main theme, Bowser's Road and both Bowser boss fights BGMs from SM64 and finally Pianta Village and the best 1-1 evaaaar, Secret Course from SMS!)
Mario Kart: Mario Kart 8 (Cloudtop Cruise, Moo Moo Meadows and Cheese Land are the ones that comes to my mind, but there are many others I like!)
Paper Mario: PM:TTYD (that title screen theme... although Sticker Star soundtrack doesn't seem bad at all, at least the title screen theme and the battle theme are nice! And let's not forget the Battle Theme and that wonderful Yoshi Village theme of Paper Mario!)
M&L + SMRPG (Yoko-RPGs): sorry, only played entirely Superstar Saga (liked many of its BGMs, from the title screen to the battle theme and Oho Oasis, even though the last two are repetitive, but really catchy!), but I must say that I really like the remakes of SS Oho Oasis and the Battle Theme in Dream Team, and that boss theme used also for Bowser Jr. is really good! And Paper Jam too appears to have a great soundtrack! The original SMRPG has a good Battle Theme and that strange Boss Theme is funny too! Yoko doesn't disappoint!
Anyway, my favorite per genre:
classic 2D Super Mario: Super Mario World
2D Mario-related platfromers (classic Super Mario series + NSMB series + Yoshi series with babies): Yoshi's Island (Flower Garden, Yoshi's Island theme (the one of the file select screen), the best castle music yet, the incredible final boss theme and much more!)
3D Mario: Super Mario Galaxy (honorable mentions: Starship Mario, Puzzle Plank Galaxy and Yoshi Star Galaxy from SMG2, Main theme, Bowser's Road and both Bowser boss fights BGMs from SM64 and finally Pianta Village and the best 1-1 evaaaar, Secret Course from SMS!)
Mario Kart: Mario Kart 8 (Cloudtop Cruise, Moo Moo Meadows and Cheese Land are the ones that comes to my mind, but there are many others I like!)
Paper Mario: PM:TTYD (that title screen theme... although Sticker Star soundtrack doesn't seem bad at all, at least the title screen theme and the battle theme are nice! And let's not forget the Battle Theme and that wonderful Yoshi Village theme of Paper Mario!)
M&L + SMRPG (Yoko-RPGs): sorry, only played entirely Superstar Saga (liked many of its BGMs, from the title screen to the battle theme and Oho Oasis, even though the last two are repetitive, but really catchy!), but I must say that I really like the remakes of SS Oho Oasis and the Battle Theme in Dream Team, and that boss theme used also for Bowser Jr. is really good! And Paper Jam too appears to have a great soundtrack! The original SMRPG has a good Battle Theme and that strange Boss Theme is funny too! Yoko doesn't disappoint!