The free program cmd-key-happy allows you to swap the Command and Alt/Option keys in any application, but in particular, in Terminal.app.

This can be extremely handy when ssh'ing into other UN*X boxes and running emacs -nw. It also allows you to have the traditional readline navigation work properly when using Bash (i.e., alt-backspace, alt-f, alt-b, etc). See this blog post for more details.

[robg adds: Installation help is available in the INSTALL file in the github repository. I haven't tested this one.]