I had been in contact with WPMU before subscribing and they told me what I wanted to get done should be possible and that I could get help setting this up:
I have both Membership and Directory installed
I want the bulk of the site to by default be viewable to, not registered, registered but not paid, and paid. But there will be some restricted pages.
One of the benefits of being paid is, they will be able to have a post in the directory.
The directory will however be visible to all.
I also want to make it so there is a captcha when they create an account.
Not sure how to set this up.