How to switch logo and menu links based on subdomain?
I am unaware of any contrib modules that do this (well, other than Domain Access), but it would be pretty trivial to write a little custom code to accomplish it.

Essentially, you would add something to your theme preprocess to detect the domain and tack on body classes.  How to do this depends on whether you are using Drupal 6 or Drupal 7.  Either method, though, would use $_SERVER["HTTP_HOST"] to detect the theme.

Then, in your CSS you would preface your logo rules with body.whatever to choose the correct one.

The menu thing is a little trickier.  You would use essentially the same logic, but set a variable containing the proper menu and print this out in your theme.  To be honest, though, I really would use Domain Access for this if you are using Panels.  The domain shows up as a panel selection rule, so you can do all of this from the UI.