So, I'm only a little better off than I started. Thanks for the Menlo font tip: it does render ñ better. It's still off on, e.g., the afore-mentioned voiced alveolar lateral affricate. I will look through the other fonts.
I guess there's nothing to do but try and integrate Yamamoto's patches into the emacs trunk. This is clearly a bug with the way NS emacs interacts with OS X.
Speaking of the patch, I didn't download 24.1.1 on purpose: the newest official version as obtained from the FTP site (
http://ftp.gnu.org/gnu/emacs/) is listed as 24.1, which is what I used. I'm not sure if a version 24.1.0 even exists... but I haven't dug through the source repository much.