Hidden options
At the team selection screen, press X to display an options screen that allows you to change such things as the difficulty, weather, stadium, and time of game.

Reset the count
While batting with a runner on any base, have the runner attempt a steal. Either go through with the steal or send him back. Quickly press Y before the view returns to your batter to reset the count to no balls and strikes.

Harder swing
Before the pitcher makes his selection, press R. When the pitch is thrown, your cursor will become small. If you hit the ball it will either be a home run, or a very hard hit.

Easy homerun
When you are up to bat with a decent power hitter, move the top of the batting cursor to where the ball is being pitched. You will hit a homerun about 90% of the time.

Bean the batter
After you select your pitch, move your cursor towards the batter and press Y.

Intentional walk
After you select your pitch, move your cursor away from the batter and press Y.

Change computer pitched shutouts
Go to your schedule screen. Press X to get the list of games and start times. When you simulate computer played games, and one of the teams pitches a shutout, you can simulate it again, until both teams score. You can also play games over when you or your opponent are shut out