Ctrl-a interferes with readline shortcuts. I've been using Ctrl-<Space>: nothing, as far as I know, binds to that.
unbind C-b
set-option -g prefix C-Space
bind-key C-Space send-prefixSame, I used C-a for a while until I found out its default mapping is jumping to the beginning of the line so I rebound tmux prefix to C-Space. Now my only problem is on a few servers where I haven't copied my dotfiles.
I’ve been using Ctrl-s for years. Nothing else uses it because it’s historically been used for terminal flow control, but that doesn’t really have much use in a graphical terminal with history and scrollbars and so I’ve never missed it. Has similar two-finger ergonomics to the Ctrl-a bind as well.
edit: oh, and I think Ctrl-space is the keystroke to get a nul character, and vi uses that character to insert the last entered piece of text in insert mode. It looks like Ctrl-@ does the same things, but tmux might not be able to tell the difference either.