Recently I've been making more use of my iMac for programming at home, and I've been struggling to get a comfortable, reliable emacs setup. Today I came across Tim Bray's blog entry on giving Aquamacs a personality transplant, and it really helped. In summary, I put these into my ~/.emacs file:
;;; AquaMacs tweaks
(setq mac-command-modifier 'meta)
(setq x-select-enable-clipboard 't)
(setq mac-option-modifier nil)
These turn the command key into a meta key, cause the emacs kill buffer to participate fully in the OSX clipboard and, ah, do something to the option key (which, now that I have command as meta, I don't use). Thanks, Tim!