How to structure database(s) for larger applications?

[eluser]pims[/eluser]
One database for each user is a crazy idea ;-)

MySQL is a powerful DB, and before you bring it to its knees, you'd have thousands of millions entries in your tables. Index properly, and I'm sure you'll never have to worry about scaling.

And as for, how to model your data, well, I tend to create a table which represent an object, and then add some tables to link the whole thing.

What kind of web app are you building ?