Best thing about Kondo is he doesn't "overcompose" or overcomplicate things. He makes very strong melodies and lets them do the talking. If any of these songs aren't actually by Kondo, let me know so credit can go where it's due.
The Top 10 Koji Kondo songs:
01. Hyrule Castle Theme (A Link to the Past) --
https://www.youtube.com/watch?v=_uR7doemZD0
So dramatic and beautiful. Its usage in Link to the Past is noteworthy in particular, in that it feels like it represents something different each time you hear it. Early, it feels big and almost oppressive, and later it feels almost triumphant. It sounds royal, epic (not a word I use lightly), intense, solemn, powerful. So great.
02. Song of Healing (Majora's Mask) --
https://www.youtube.com/watch?v=7G_aaak-tDE
There is so much emotion wrapped up in this song. It fits the melancholy world of Majora's Mask so effortlessly that it basically defines it. It's beautiful.
03. Castle Theme (Super Mario World) --
https://www.youtube.com/watch?v=fdmS4ndSAT8
Every part of this is incredible. The "spooky" feeling at the beginning transitioning to intense drama midway through is my favorite part (0:40 onward)... it just propels you forward, that descent into the "madness" and "despair" of the castle.
04. Intro Theme (Legend of Zelda) --
https://www.youtube.com/watch?v=uyMKWJ5e1kg
This song basically convinced me that games were something special. It instantly transported me into the world of Zelda. As with many Kondo themes, he has a dramatic, solo instrument transition to accompaniment with a steady march that makes you feel as though adventure is afoot.
05. Final Battle (Ocarina of Time) --
https://www.youtube.com/watch?v=gmL3xSeAmsw
I can't listen to this without getting chills. Kondo knows exactly what to play here... it's dramatic but understated, a chorus over a rolling snare beat. The perfect accompaniment to the most perfectly executed final boss battle of all time.
06. Final Hours (Majora's Mask) --
https://www.youtube.com/watch?v=Lcpd0lhYMQI
Nothing captures "the end times" like this song. Rather than make you feel like a hero, it makes you feel like it's just over... nothing you can do, with only despair and sadness left.
07. Gerudo Valley (Ocarina of Time) --
https://www.youtube.com/watch?v=PXCzilsqThA
This song is the shit, and everyone knows it.
08. Bowser's Road (Super Mario 64) --
https://www.youtube.com/watch?v=eM5nOBgpDsQ
Fantastically redone in SMG2 here:
https://www.youtube.com/watch?v=pvH5BTOf2qk
Kondo's instrument choices are so good in Mario, they're so different from other games but always manage to sound so uniquely "Mario." This one makes Mario feel like he's on a journey against all odds, a marathon of skill and effort.
09. End Credits (Super Mario 64) --
https://www.youtube.com/watch?v=eVKj3u8JUm0
I can't help but feel happy listening to it. It makes me just want to start another play through immediately.
10. Staff Roll (Ocarina of Time) --
https://www.youtube.com/watch?v=NPjLgDF1hUg
At the end, when Navi flies away, the music always makes me want to cry. So touching. A great way to close out the game, taking you back through your journey in a way that is both happy, sad, nostalgic and proud.