Believe it or not the famous Konami Code works here as well. Though it won't give you extra lives it will give you extra continues. Just enter the following code at the title screen.
4 Continues instead of 2 - Up, Up, Down, Down, Left, Right, Left, Right, B, A and Start.
Game Genie Codes
ZENOATGO Pick up 10 weapons only
ZUNOATGP Pick up 50 weapons at a time!
GXSOUAST Don't take most damage
SXVZGSOO Don't take damage from non-killing seaweed
AEOOGTZA Full energy boost from pizza slices
GPUOLNZA 20 missiles on pick-up
TAKOPYLA Double rope on pick-up
SXVXTLVG Never lose rope
Giant Mouser boss glitch
The Giant Mouser at the end of level 4 can be beaten even more easily than normal with this trick. Just stand under him and wait for his mouth to open. When his mouth opens to reveal the "weak spot", pause the game. Unpause the game, and the Mouser's mouth will be closed again, but his weak spot will be slightly visible from behind his mouth. You can now hit it to cause damage while his mouth is closed! Repeat this every time he opens his mouth for an easy victory.
Kill Rockstedy Without taking a hit.
When you fight Rockstedy jump on top of the ledge on the right side of the screen, switch to Donatello and just attact downward. Everytime Rocksteady jumps he will take damage and you will get by without a scrape. This will work faster if you time your attacks with his jumps.
Kill Shredder while taking little to no damage
When you make it to the final boss (Shredder) all you need to do is have Donatello or another Turtle that has the scrolls and position them on the lower right side of the screen (not on the ledge). When Shredder comes close jump up and attack, this will knock him back and he will then jump up towards your Turtle again. Just keep jumping and attacking in that one spot and he will never get close to you because the ledge in front of him will prevent him from getting close enough to touch you. The only thing you'll have to worry about is his gun which he only fires while stationary, so just jump over what he shoots at you.
PC version
In PC version do this: A + S + D + F + G + H activates a walkthrough-walls code and pressing Q + W + E + R + T + Y + U + P activates an invincibility code.
Remove Crushers in Level 3
Go to the third level and hop in the Party Wagon. Whenever you see a pesky Crusher drive around, press SELECT. You will exit the car, and the Crusher should vanish from the screen.
Secrets
Easy way to restore power
Find a doorway that has a pizza slice or full pizza right at the beginning. Enter, grab the pizza, and exit. If you go back in the pizza will regenerate. Use this to restore power to all your turtles.
Share Boomerangs
When you get the boomerangs, throw up to 3 of them in the air, then switch turtles, and have the new turtle catch them. The new turtle will be able to use those boomerangs without having picked up a boomerang icon.