Okay, looks like the least common denominator is working best, in my
testing, setting TERM=screen works in all of my test scenarios.

TERM=screen
 * Working: vim/tmux, vim/screen, mutt/tmux, mutt/screen, 256color2.pl
 * Broken: none

TERM=screen-256color
 * Working: vim/screen, mutt/screen, mutt/tmux, 256color2.pl
 * Broken: vim/tmux

TERM=screen-256color-bce
 * Working: vim/screen, mutt/screen, 256color2.pl
 * Broken: vim/tmux, mutt/tmux

TERM=screen-bce
 * Working: vim/tmux, vim/screen, mutt/screen, 256color2.pl
 * Broken: mutt/tmux

vim/tmux:

** Attachment added: "256colors2.pl"
   
https://bugs.launchpad.net/ubuntu/+source/byobu/+bug/908766/+attachment/2675813/+files/256colors2.pl

** Changed in: byobu (Ubuntu)
       Status: Incomplete => Fix Committed

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https://bugs.launchpad.net/bugs/908766

Title:
  byobu changes background color in applications

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