Have a lot, but here are my favorite of favorites and the reasons, there will be a battle theme, a route theme, a legendary battle theme and a Champion theme.
Gym Leader: Last Pokemon:
https://www.youtube.com/watch?v=ydWLd2LyvwE&feature=related
It's the main pokemon theme. The one that's heard in the intro, but remixed into a battle song just for taking down the Gym Leader. It's fun to listen to, and is quite fitting. I wish I could hear it more then the Gym Leaders, because this is just awesome music in general, that final stretch, you can make it! Go!
Diving Theme:
https://www.youtube.com/watch?v=nYsrhdJXtEQ
I don't know what I like about this. It goes together so well with it, sounds very fitting underwater, actually. A semi-calming theme that also sounds mysterious at the same time. This is just a good-sounding piece. The sounds, I really like in this.
Non-Main Legendary Theme:
https://www.youtube.com/watch?v=yFpAFQH-mJw
This one is just epic. It was tough to think of which one to put in. But overall, I chose this one, because I simply thought it fit a little better. It reminds me of a dungeon theme in MD2, also, and that's a plus. Both legendary themes really are good though, give them a listen.
World Champion Theme:
https://www.youtube.com/watch?v=HPRLhtoZ0M4&feature=related
And there you go.