Yea, you certainly in a tough position, but in a much better one than those who did not get into any school. It sounds as though you really want to go to Fuqua over the others (I would agree with you on that). Both Thunderbird and ND are good schools, however I hear that Thunderbird is going bankrupt and is having faculty issues. This is just something I heard through the MBA grapevine, but if it is true that's kinda ironic for a b-school, dontcha think? ND has a great alumni network, but I view it as more regional (i.e. Midwest) compared to Duke.
My suggestion is to pick either ND or Thunderbird and pay the deposit for it if you haven't already. They are both offering similar tuition compensation, so that should not be a deciding factor. Then, work diligently to get yourself admitted off the waitlist at Duke. I don't know much about the waitlist process at Duke, but here is what I can suggest to you based on my experience (waitlisted at Chicago):
1A. call for a feedback session to gain insight to your weaknesses or other areas that need bolstering. Also, make sure they know that you want to stay on the waitlist.
1B. if feedback sessions are not available for waitlist applicants (most schools do not offer these), have an in-the-know person, such as a current MBA student or faculty, take a look at your application package instead.
2. talk to current students at Duke about your situation and gain insight from them. Also, try to talk to someone who got in off the waitlist. This is extremely valuable.
3. With all this info, craft an additional essay, addressing your weaknesses that were not addressed before, updating any new and pertinent info, and stating your continued interest to go to Duke. Say something like, "if you admit me, I promise I will enroll" somewhere in there. Also, additional letters of rec could be useful if it can help bolster a weakness or provide valuable info or another side of you that was not previously illustrated.
4. Make an appointment to visit the school again and make sure they know you are coming. They will make record of it and put it in your file. This will show continued interest.
Again, I am unsure as to how Duke administers their waitlist, but I hope this helps!
Good Luck!