Kanto: Ash vs Blaine, round two (Charizard against Magmar) - no contest!
Orange Islands: Drake (I haven't watched the OI episodes in years, and this is the only decent battle I can recall)
Johto: Ash vs Gary at the league, long awaited, well delivered.
Hoenn: Ash vs Katie at the League (this one has always stood out in my mind as being the best battle of the league.)
Battle Frontier: Ash, Brock and Forrest against Jessie, James and Meowth (or Donphan, Steelix and Geodude against Aggron, Charizard and Meowth) This is probably the last time I had fun watching Team Rocket. And Geodude was given his first moment to shine in... ever!
Sinnoh: Ash vs Paul at the league - Inarguably my favourite battle of all time. Two rivals pushing each other to the very limits of their knowledge and skill, and I thought that it played out rather well.
Unova: Hard to say, as I don't think any of them came up to previous standards, but I think that Ash and Stephan's battle at the league was the best of the bunch, especially with Palpitoad debuting its Sludge Wave attack. I would add that Ash's Charizard against Iris's Dragonite had the potential to be a very close second, but I was disappointed that Charizard was for some inexplicable reason given Slash and Wing Attack as "new" moves, and the battle was called off. It's still my second favourite, but not as close.
For anyone interested, by friend code is 5257-9947-2315. If anyone wants to add me, remember to PM me so I can add you too.
My friend safari contains the ground type pokemon Phanpy, Marowak and Palpitoad.
Current Y team consists of Delphox, Pidgeot, Raichu, Simipour, Charizard and Gogoat.
In training: Wartortle, Bulbasaur, Chespin, Froakie, Combusken, Pangoro.