Beating the big superboss at the end of Air Zonk is a lot easier than it looks. Don't let his size intimidate you.
The first part, where he's in three pieces, you simply dodge the shots from the first two, and hit the third with your charge shot, which should wipe out all of the homing missiles. When he joins together to form his final form, what you want to do is pummel him with charge shots exclusively; don't wait for the bomb because it takes too long to charge and doesn't do enough damage anyways. He attacks with a series of patterns...knowing which one to look out for is the key. His only really challenging attack is his homing missile shot...if you know when it's coming, you can nail the missiles with your charge shot and wipe them all out. It will always come after a specific attack (it's been awhile, but I believe it comes after his attack where he shoots orange cubes at you). Don't worry about the green things that circle you and block your shots...your charge shot will disperse on it, hitting him multiple times. The charge shot will also go through most of his attacks...except his lightning bolts, which will eat the shot. Fortunately he doesn't use the lightning bolts very often. But whatever you do, stay to the left of the screen, that way you have enough time to react to whatever he's shooting at you. And Covell's suggestion about exploiting the invincible time after you die is solid advice...you can get in quite a few free hits there, just don't stay there too long or you'll lose another life.