I wouldn't call it the single best song in the games, but I think Black/White's theme for the Badge Check Gates and Victory Road is great. Largely because of the buildup as you progress through each gate, adding a new instrument each time until you finally get the full song, including the recognizable melody, that plays throughout Victory Road proper.
But I might be biased because I just got there in White, so the song's been on my mind.
https://www.youtube.com/watch?v=O1Bpia5XVmo 
