Fable two - put down the controller for "final boss".
Twilight Princess - pull out fishing pole to distract ganondorf to get free hits with master sword. I believe this works for Skyward Sword as well.
Metal Gear Solid second Sniper Wolf fight - from the beginning, go all the way to the right where you're behind a wall of snow. Pull out the remote control missiles and controls them across battlefield and hit her with them. Rinse and repeat.
Kingdom Hearts 2 bosses - spam reflect when on the defensive, murders them quickly. Also, to defeat Lingering Will easily, make your air combo a one hit combo and spam air attack. He gets stuck in his recoil animation while you spam the air attack.
Final Fantasy X end game bosses - Yojimbo's instant kill move Zanmato. Just pay him the minimum amount for it and hope it happens. If not, then reset game and try again. The game has a hidden tally system of how many times you use the move. The more you use Zanmato, the more likely Yojimbo will use it when summoned. Sometimes for free I do believe.
Sonic 2 chemical plant boss - before Eggman pops up from the right, if you time your jump just right you'll be right above him when he comes on screen. Here you can continually bounce on his head 8 times quickly. Make sure to count so you can move to the left on the 8th bounce because if you don't you'll fall into the water and die upon his death.
That's all I can remember right now. If I remember more I'll edit this post.
Edits:
MGS3 the End boss - as some have said about the End, you can completely skip the fight if you want. After going through the swamp area and before the cutscene with boss and Volgin, you can take a small detor path to get a sniper rifle. After the cutscene mentioned, The End will be on the pier where the Boss and Volgin was for like a min before being wheeled away. If you take out your sniper rifle and shoot him, he explodes and dies. Watch out though cause a wheel from the wheelchair will come flying to hit you and I believe kill you, but it can be dodged if fast enough. Now, in the boss fight area for the End, you will have Ocelot's group in the area to take you down. I think there is like 8 of them and you have to take them out before you can move on.