mine was when i battled red in i think it was leaf green that pokemon battle was actually challenging

My hardest battle... None of them? Seriously. I don't rush through RPGs, I train so that I'm ready for each challenge.
I suppose maybe if I brought the wrong Pokemon with me to the Elite 4 I would have had a tricky time, but that hardly happened.
I suppose my hardest battles have been against lengendarys.
I'll be either too strong for them and kill them or they won't hurry up and get in the damn ball!

My idiot little brother who thought it'd be fun to go through the Sinnoh elite four SEVEN CRAPPING TIMES.

He ended up with 85+ Pokemon, while I was much lower then him.

I've GOT to get my team to Lv. 100.

Battle Factory on Platinum, don't remember full teams, don't remember what my current winning streak was, all I know was my bronzong was unintentionally sent out against my opponent's Milotic, I presume because either it was my last pokemon, or my others would have done worse. It knew two actual attack moves: extrasensory, was it, or zen headbutt? can't remember, but it was that and uh, flash cannon? I think it was flash cannon. Anyways, it knew one psychic move that was too weak to deal good damage, and a steel type move. Oh, and rockslide, forgot about that one. Its fourth move was Trick Room. The opponent's Milotic knew Aqua Ring, Confuse Ray, Toxic, and Double Team, I think. It's been a while since I had this battle, but none of it's moves were directly offensive. So, my opponent's Milotic confused Bronzong, and then used Aqua Ring. It then commenced with a long string of Double-Teams, to the point where my hits were few and far between, augmented by the fact that I was confused half the time, and when they did hit, they did so little damage that Aqua Ring easily restored all of its health back. Needless to say, I was actually desperate for Bronzong to run out of PP. So when it finally did, it misses a couple of times, but I finally faint milotic. And faint myself with the recoil. Guess what? Bronzong was my last Pokemon, but milotic was not my opponent's last. I was very, very mad.

When i took on the last of the elite four in every pokemon game.

Actually, none, because I level up all my Pokemon each time I meet a new trainer, reach to a new area and if an enemy attack decreases my Pokemon's HP by 1/3.

The hardest battle for me would be Trainer Red in Pokemon Crystal all his Pokemon are very strong.