I finally found a reference that helped me out. I understood that the problem was conflicting ideas about modifier keys; gnome-terminal uses Mod1, but Emacs uses Mod4. What I didn't know was something I found out here, namely that Emacs only uses Mod4 if it exists. So a better solution for me is to simply clear Mod4 altogether, and both programs happily honor Mod1. (This leaves xterm hosed, but if gnome-terminal works, then I don't need xterm anymore.)
My resulting .xmodmap looks like this:
remove Lock = Caps_Lock
keysym Caps_Lock = Control_L
add Control = Control_L
This makes my PC keyboard behave sensibly. Alt is Meta. And Caps Lock is consigned to oblivion and the large key that used to have that function is now much more usefully assigned to Control.
I'm posting this here in case anyone else has struggled with this particular annoyance in the past. The clear Mod4 trick was the surprise ticket. (What I'd really like is a way to tell programs which Modifier is "really" the Meta key, given that the programs can't seem to agree on this. And with just one preference -- redefining the numerous bindings in emacs for each sequence, while possible, is not my idea of a fun thing to do.)
The other thing I'd like is a standard way in illumos/opensolaris to integrate .xmodmap. Linux/Ubuntu seems to detect my .xmodmap and handles it nicely.