Let’s do it more simply.
If you are using tmux below version 1.7, append next line to ~/.tmux.conf:
bind-key C-s run "for i in $(tmux lsw|awk -F: '{print $1}'); do tmux movew -s \$i; done"
You could sort all windows, by typing PREFIX-KEY, then Ctrl + s.
Else, if you are using tmux version 1.7 or above, as already everybody says, append next line to ~/.tmux.conf:
set-option -g renumber-windows on