Start game as usual, go to to the Password section under Options and enter the following codes:

Effect Password

Alternate costume for Donatello1 LMSSL
Alternate costume for Leonardo1 MSRLR
Alternate costume for Michaelangelo1 MMMSL
Alternate costume for Raphael1 SMLSR
Attack power up for Donatello DRLDS
Attack power up for Leonardo LMLSD
Attack power up for Raphael RDSRL
Alternate attack sound effects SLSRS
Defense doubles for Donatello LRLDD
Defense doubles for Leonardo SSRSL
Defense doubles for Michaelangelo LSSDR
Defense doubles for Raphael DSRRS
Defense power up for Michaelangelo MSRMM
Master Splinter in story mode LDRSM
Playmates toy database LSDRM
Power up effects double for Donatello SDDLS
Power up effects double for Leonardo LDDRS
Power up effects double for Michaelangelo LMLMS
Power up effects double for Raphael DLDRS or LMMDR
Unlimited fire shurikens and all food is pizza for Michaelangelo MDMSL
Unlimited Shurikens for Leonardo SRRDM

Letter abbreviations are as follows:

M - Michelangelo
D - Donatello
L - Leonardo
P - PiZZADOX
R - Raphael
M - Master Splinter

Challenge mode:  Successfully complete story mode as Raphael, Donatello, Michaelangelo, and Leonardo.

Casey Jones:  Successfully complete level 1 as Raphael to unlock Casey Jones in versus mode.

Evil Turtlebot:  Successfully complete level 3 as Raphael, Donatello, Michaelangelo, or Leonardo to unlock the Evil Turtlebot in versus mode.

Hun:  Successfully complete level 6 as Michaelangelo to unlock Hun in versus mode.

Oroku Saki:  Defeat Saki as Raphael, Donatello, Michaelangelo, or Leonardo to unlock Oroku Saki in versus mode.

Shredder:  Defeat Shredder as Raphael, Donatello, Michaelangelo, or Leonardo to unlock Shredder in versus mode.

Splinter:  Successfully complete Dojo level 3 as Leonardo to unlock Splinter in versus mode.

Yoshi Hamato:  Successfully complete Challenge Mode as Raphael, Donatello, Michaelangelo, or Leonardo to unlock Yoshi Hamato in versus mode.

Alternate costumes:  Set the system date to December 25 to see the turtles with a Christmas theme. Set the system date to October 31 to see the turtles with a Halloween theme.

Unleash the Secret of Gembu Beat the third Dojo Stage with all four turtles to learn the Secret of Gembu maneuever. Use the move to damage everyone on the screen. You'll have three opportunities per level to use it.