Oh, mine is easy. In "Megaman Battle Network 3 Blue Version", the last Boss, Alpha, was the toughest mother freker I had to beat.
Ok, look, he had 2 kind of shield before you attack him. If you broke the first one but didn't break the second one in 5 seconds or so, it regenerated and you had to break both of them AGAIN!
Plus, his attacks aren't made to take a lot of your health, but are used to PREVENT you of using your battlechip before his shield gets back-up. So basically, if you didn't use your 30 battlechips efficiently, you're doomed.
Here's the image of the incredible beast, ALPHA!
I wanted to show the video of the battle, but every one of them showed the player beating Alpha rather easily, so I won't show one ._.