I use Emacs on and off, as well as Vim, and the key I've settled on for tmux prefix is ^q. It doesn't conflict with anything useful (that I've found anyway) and it's easy to hit with a caps lock as control.
For the record ^b is also move backwards by character in basic readline bindings (so it works in Emacs, on the command line, and everywhere on OS X). I've always found it baffling the programs like tmux and screen override readline bindings. Shouldn't those be on the list of bindings to never override?
In zsh (or at least with my configuration, which is prezto with a few plugins), Ctrl-q lets you "stash" your current command.
Say that you are typing some really long, complex command, and suddenly you realize that you are in the wrong folder. You press Ctrl-q (which clears the command and "stashes" it), then you cd to the right folder. As soon as you return to the prompt after issuing your cd command, your really long, complex command is back just as you typed it.