During normal gameplay, Phineas is only able to show up in the city from 9 AM to 7 PM. However, the game contains unique versions of his music box theme for the night, late night, and early morning variations of the city's background music. These can only be legitimately heard by staying in the city plaza during the turnover to 7 PM and remaining there indefinitely. Because the game world reloads itself at the start of each new day at 6 AM, Phineas will eventually be forced to leave at that time, preventing the player from hearing his music box cycle back to the daytime variant.

In the surveillance center, when the alarm goes off, Resetti will call out "Code 64." This is thought to be a reference to the Nintendo 64.

During development, the development team explored the use of WiiConnect24 in the hopes that a player could visit a friend's town even when he or she was not playing. The friend could then leave letters or gifts. Additionally, they planned to use Wi-Fi Connection to allow simultaneous play. It's unknown why these ideas were scrapped.

Ankha the cat's snake charm on her head was removed and replaced with a head pendant for unknown reasons.

Totaka's song can be found in this game. At the beginning of the game, while you are choosing your town's name / your name / your gender, wait a few minutes and you can hear the bus driver whistling the tune.

Every New Years Eve, the player will receive a New Years Shirt with the upcoming year's Chinese zodiac animal. Oddly there are shirts for the years 2000 through 2008, which are impossible to obtain without altering the internal game clock. The special shirts stop at 2035.

In the City, there are two traffic cones on the far right side. On some nights, after 8 o'clock, one of the cones can be moved and the Reset Surveillance Center can be accessed. There, Mr. Resetti can be found in his whole body. He bribes the player with a silver shovel and says not to tell anyone. This explains why he knows when you haven't saved.