The one I still remember vividly, even though it happened quite a long time ago was my battle with the Star Magician in Golden Sun: The Lost Age. If you are unfamiliar with the games, they are an awesome series of jrpgs; The Star Magician is one of the four optional boss fights and although it isn't the toughest, it was the closest fight I've had in Golden Sun (I never did manage to beat Dullahan). You can skip to the last paragraph for the short version.
I went into the fight without knowing anything about the enemy. It turns he was a relatively powerful enemy by himself, but he also had the ability to summon four magic helper balls with various abilities. If any ball were destroyed, the Magician would quickly summon more to replace them. Their abilities ranged from providing the Magician with healing and huge defense boosts to blasting all my party members with high level magic attacks. I quickly found out that their defense and healing powers were too strong and slowed my attack, so I was forced to keep destroying the balls until they were all replaced with damage dealing ones. This meant I took huge amounts of damage most turns, but now my attack was unhindered. I focused all of my attacks on the Magician alone; I couldn't risk having a destroyed ball being replaced by a healing one.
The battle was long and both sides took major damage. I kept taking casualties and my attempts to revive them for long periods of time continued to fail due to the massive incoming attacks every turn. I soon realised that in a battle of attrition, I was the only one who could lose. From this conclusion, I decided to go on a major offensive, ignoring revival. I needed to keep up the damage no matter what, my healers could only draw out the battle for so long. After this increase in attack, the Magician didn't last too long, but by the time he was defeated, I had lost most of my party. I had hoped that defeating the Magician would cause the balls to die too, but no such luck. 4 lightning balls remained, which meant 4 spark plasma attacks per turn; they took their toll and soon I was down to just Mia and Garet (both of whom I didn't use much). However, the balls didn't have much HP left either, I'd learnt their approximate HP from killing so many of them already; I only needed a few turns.
Perhaps two turns later, Mia's healing could no longer keep up with the damage and she fell. A badly beaten Garet was the only one standing. This was the last attack, there was no way Garet could survive even one more spark plasma, let alone four. One last attack, one last chance. How much HP did they have left? Surely they must be close to death by now. Would this be enough, or would I have to go through the whole battle again?
Well, long story short, I beat the Star Magician by the skin of my teeth, the very last possible attack finished off those dirty purple lightning balls, and Garet actually managed to do something good for a change.