Starting with tmux 1.6, you can use the session option prefix2 to specify a second prefix key (e.g. in ~/.tmux.conf):
set-option -g prefix `
set-option -g prefix2 C-a
Note: If you have any bindings or script that use the send-prefix, you can use its -2 option to send the key assigned to prefix2: send-prefix -2.
Prior to tmux 1.6, the prefix option accepted a comma-separated list of keys:
set-option -g prefix `,C-a