After figuring out a config mistake by me (I forgot to tell Compiz to use the GConf backend...) I've got Compiz back up and running again on my Arch box.
Except for three niggling probably minor, but still slightly annoying ideas.

First is the mouse cursor. *Most* applications use whatever I've set in Gnome Appearance Properties. gnome-panel and a few others, when under the influence of Compiz, instead draw the ugly default black pointers. I've yet to find a fix for this one.

Second is the GTK theme. The 'gtk-window-decorator' (I don't like Emerald) seems to happily pick up the GTK and Icon themes I originaly had when I activated Compiz. They don't pick up any changes, however, and don't apply them to any window except the Gnome Appearance Properties. Everything else remains totally unaffected.
Update: Restarting seemed to be all that was necessary for this one to be solved.

And last, and more of an 'I want to be able to...' one, is on most other distros, scrollwheel on the desktop changes desktop. Except for me, it doesn't.
Update: Turning on the Viewport Switcher plugin solved this.

They're all ignorable ones, but they're ones I'd like to try and fix if I can.