Use a text editor such as notepad to edit the saved game file in the game directory. Insert the following lines in the file to unlock all bonuses.

[Slot 1]
EasyMode=1
EndingAvaliable=Yes
Entrance=1
GameInProgress=Yes
HasPracticeBall=1
HasNormalBall=1
HasIronBall=1
HasSpeedBall=1
HasGlassBall=1
HasYogaBall=1
HasPatheticBall=1
HasJumpBall=1
HasFreezeBall=1
HasFreeBall=1