It’s really all described in the documentation.
Anyway, here’s how you do it:
$user = new User();
$user->username = Input::get('username');
$user->password = Hash::make(Input::get('password'));
$user->save();
$user->roles()->attach($roles);
The important part is that you have to save the user before attaching (using attach()) the roles because otherwise the user doesn’t have an id yet to be used in the pivot table.