Multi users, the users must not be able to see each other's data.
In the past I done one database and the select statements had the users ID in it, so only the user's data was returned. The user's data is sensitive and users should never be allowed to see each other's data.
Some sites I've notice have different directories for each user. I am curious why.
first of all its up to you how to restrict every user to their own data and how. mostly those site are using same database and tables for all users. the directory or path you see after the actual domain name is not a real directory often, they use URL Rewrite to make it more readable and SEO friendly.
however you can perform different kinds of validations while working with database.