Automatically Log in User In my Controller I created a script to add a user to the database, is there a way I can automatically:

1) Log them in and 
2) Set a permanent session cookie or similar?

I basically don't want the user to have to ever log in and we will be creating the accounts for them.
You're probably looking for a combination of:

craft()->userSession->login()

or

craft()->userSession->loginByUserId()

along with setting the userSessionDuration config setting to a really high value.