For facilities, the "Facility Group" seems to control the order within the game. Within a particular Facility Group, I would guess the order to be the same as in the file, but I haven't verified that.
For components, I would guess that the "General Group" field works similarly to "Facility Group", but again, haven't verified that.
As for how I'm doing the sorting, it can currently be sorted in ascending or descending order by name or by facility group. I'm using some slightly modified code I found on Microsoft
http://support.microsoft.com/kb/319401
But yes, now that I think about it, alphabetical sorting doesn't make as much sense. I think I'll modify it so you can drag the facilities to whatever order you wish and get rid of the alpha-sorting.
Or maybe I'll just add some info to make it know what order to put it in the file, because the alpha-sorting by name or facility group is actually kind of useful as well. Will have to think a bit more on this one.
Thanks for the suggestions!