tl;dr Putting config files in a folder under
/App_Config/Include causes them to be patched in last.
Following an answer by @Bruud on Stackflow a few months ago I found out that it is possible to organise patch config files much more neatly. It was also mentioned as a passing comment on one of the recent Google Hangout highlighting the changes in Sitecore 7.X.
I’ve just started working on a few project from existing vendors and noticed the common patch file naming convention to ensure custom changes are applied after the standard Sitecore configs in
It turns out that you can simply put your custom configs in a child folder and Sitecore will include them after any files in