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Secrets brought to you by 
300000 Easy Zenny
First do the job "Legendary Tomes". Once you have the tomes don't go back to the Navi, instead go to the teachers lounge. Look at the back shelf and examine the strange orange statue. Theres a code in the statue that matches with the tomes and the data is 300000 zenny.
Secret Area
Once you complete the game by defeating the final boss, wait until the credits roll and the title screen appears. There should be a star next to 'continue'. When you continue the game, it will continue from the spot where you last saved as usual, but you will now be allowed access to the Secret Area, which is located in the Ura-Internet square. You can only get there by pluuging into the computer under the hot springs. You will need 100 standard chip entries in your library to enter.
Secret Boss
After you complete the Secret Area by defeating Serenade, put at least 300 BugFrags in the Trader, then leave the internet. When your return to the Bug Trader, Forte will appear, fused with Gospel, and attack you. If you defeat him, you will get the Forte chip.