to get new R help windows to open in new frames for Aquamacs:
-------
(require 'ess-site)
(setq inferior-ess-own-frame t)
(setq inferior-ess-same-window nil)
;;create a new frame for each help instance
;; use this one if each help window goes to a new frame
(setq ess-help-own-frame t)
;; use this one if you want all help windows into one frame!
;; (setq ess-help-own-frame 'one)
--------
and I added the following lines to the site-start.el file in the site-lisp directory:
--------
;; load site-start.d/*.el
(mapc 'load (directory-files
"/Applications/Aquamacs Emacs.app/Contents/Resources/site-lisp/site-start.d"
t "\\.el\\'"))