All three honor societies?

I am a senior and I am in NHS, NEHS, and Mu Alpha Theta.

I know that this looks very good on an app but which one will look the best? Is it National Honor Society, Mu Alpha Theta, or National English Honor Society?

Are you planning to only list one, or wondering what order to put them in?
I don’t think it will make any difference at all in your application.

I don’t actually think being a member of an HS is that big a deal on a application. Assuming you are selected based on your academic achievement/school activities - these things should already be evident on your application. It’s a nice acknowledgement in your school of that achievement, but makes little difference to college admissions. If you have a significant role in activities/events of the HS (planning, participation, etc), then THAT will carry a bit more weight on your app, and that is the one that will “look better”.