I'm including my favorite track in each game so if you want to hear what I think is the best from each game, you can check those out.
NES: The Legend Of Zelda. The main theme in the game is amazing, especially for composing VG music at the time. (Runner Up: Super Mario Bros. The Overworld theme is catchy to this day)
SNES: Super Mario World. I love the Bowser's castle theme especially. (Runner Up: The Legend of Zelda: A Link to the past. Dark World rocks.)
GBA: Super Mario Advance 3: Yoshi's Island. I couldn't fit the original on the SNES list. Haven't played that many GBA games. This one has such a catchy joyful soundtrack, especially Athletic.
N64: Super Mario 64. Bob-Omb Battlefield is my favorite from this game. Awesome soundtrack all around. (Runner Up: Ocarina of Time. (Gerudo Valley is my favorite from this game, not the only great one though.))
Gamecube: Double Dash 'Circuit theme' is a classic (Runner Up: LoZ: Wind Waker. Love Dragon Roost Island)
Wii: Super Mario Galaxy/Super Mario Galaxy 2 (Tied) Amazing soundtrack for amazing games. These 2 are tied for my all time favorite soundtracks. My favorites are Egg Planet, Gusty Garden, and Sky Station.
Wii U: Mario Kart 8. Such an amazing jazzed up track, full of retro remixes and new compositions. My favorites are the F-Zero themes, Electrodrome, and the Hyrule circuit tracks. (AMAZING!!)
(Very Close Runner Up is a tie between DKC: Tropical Freeze and Yoshi's Woolly World. Both are my favorite games and soundtracks in their respective series. Snowmads theme, and the main Woolly World theme are my favorites here.)
Switch: LoZ: Breath of the wild, I loved this soundtrack. It has the main theme as my favorite. Every single one of the many tracks felt like well polished and magnificent compositions. (Runner Up: Super Mario Odyssey. the Fossil Falls theme is amazing, as is the rest of the game.)
I haven't played to many on other platforms besides PC, so I'll have an 'other/multiple platforms' category.
Other: Shovel Knight: Treasure Trove. I only found this game last year, and the soundtrack is amazing. I love all of them, but 1,000 Leagues Under, Strike The Earth, and Main Theme are my favorites. I HIGHLY recommend listening to this if you haven't yet. (Runner Up: Minecraft. Such a peaceful soundtrack. Especially the ones in Alpha Album. Wet Hands is my favorite from this game.)
There you go.