I’m not quite clear on where to edit the outgoing invitation emails.
Should this be done by editing the resx file in the 12 hive, or in the list on each and every site collection, or just on the site collection at the root of the web app?
At every site level where you break permission inheritance and therefore setup delegation, you can go to Site Settings and click on Delegation Mail Definitions under the Delegation Configuration section. This is where the email definitions are stored and you can edit either the Subject or Body. The body can contain any valid html and both the subject and the body can include tokens for dynamically generating things like site titles or urls. The complete list of available tokens can be found in our online documentation at http://help.sharepointsolutions.com/products/excm/Configuration_Emails.html.
ok, so its configured at a site collection level only?
We currently have approx 40 site collections, and this is likely to grow.
We don't really want to have to make a minor change to, say, some wording, in that many site collections.
You can modify the e-mail definitions used by future sites by modifying the mail body definitions in the delcore.resx and delcore.en-US.resx located in the '12\Resources' directory. These files are identical so after creating the first file you can simply make a copy and rename the file.
If you want to update your existing sites with the new definitions you can either edit them by hand or deactivate/activate the Delegation Web Components site feature. You may find a command line or PowerShell script could make this task easier.