It's hard to narrow down one favorite or even a few. But I do think David Wise is my favorite composer. Busted Bayou and Wing Ding from DKC Tropical Freeze are fantastic tracks, and of course everyone loves Stickerbush Symphony. Also, while it wasn't by Wise, the first rocket barrel theme from DKC Returns is amazing, the way it starts out and 5/4 (which is not a common thing to see and tricky to play) and then changes to 4/4.
Yoshi's Island's athletic theme may be my favorite Mario series tune, but I do think that, at least with the 3D games, the music improves and improves with each one. I was very happy when they brought orchestrated music to Mario Galaxy and even more thrilled with the big band music in 3D World. And if Jump Up Superstar is any indication, I have a feeling Odyssey will be incredible music-wise.