Which location to visit, character to interact with and dialogue are all choices the game.
A choice might not have an obvious or immediate effect. Choosing to spend time with a specific character means you also chose not to spend time with another character. Unless you promised to spend time with that other character, they won’t know you could have spend time with them.
Besides the obvious effect of increasing or decreasing your Affinity and Persona scores, choices are also remembered. Certain choices can have a lasting effect other than simply altering your current score.
An optional event on the first Friday involves Cynthia Cooper, your best friends mom. During the event she may ask if you're a virgin. Your response will have a bearing on her future attitude towards you.
These remembered choices will affect dialogue, choices and even entire scene availability as you progress through the game.
Your affinity and persona can also affect which options are available.
If only one option is available, it will be automatically selected without offering the player a choice.
Version 2 introduces the disabled menu choice. The game will show you the other options(s), but not allow you to select them.
-Girl Choice-
A girl choice will force you to choose between two women. With options increasing the affinity with one woman, whist decreasing the affinity for the other.
At the start of the game you have an event involving Catherine and her mother Victoria. Being sarcastic towards Victoria will increase your affinity with Catherine, at the expense of your affinity with Victoria. Conversely, being nice towards Victoria will have the opposite effect.