To set the printer defaults you go in Windows to :
Start > Devices and Printers then right-click the printer and go to Printing Preferences , set what you want and select Apply
So at this point, any application that is not currently open on the PC, when you open a file and select File>Print it should have those preferences by default.
But if you change those settings, most applications will hold the changed settings in the application until closed. For instance, you open a pdf in reader and print a job and choose color, if you don't actually close all open Acrobat/Reader windows before you open the next pdf it will hold that color setting (Last used settings)
The most common oddity is Windows Picture and Fax viewer which seems to have its own rules, it will always seem to be the last used settings no matter how many times it has been closed.
Then you have the applications like Indesign, Where the driver will hold its own defaults like it should for each new opening, and hold the last used settings if it is not closed, but there are also the settings that Indesign pulls from the driver in the File>Print window, those settings will over-ride the driver settings so if they are set to something different, those settings will honored over what is in the driver.
I ran an experiment with Excel 2007 with several sheets, mixing up properties.
Excel seems to save the printer property in the file, sheet by sheet. ABC.XLS originally has 2-sided set for all four of its sheets. While on sheet3 I change to 1-sided, print, save, close Excel, reopen; and Sheet3 now comes up as 1-sided, and others sheets still come up as 2-sided.
Also: before all this, if I printed entire workbook, it was all two sided, that is, sheet1 is 1 of 4, other side of it is sheet2 as 2 of 4, next sheet has sheet3 as 3 of 4 and sheet 4 is on the back of it. Now, after saving 1-sided to sheet1, printing entire workbook yields sheeet1 and sheet2 on 2 sided, sheet3 alone, then sheet4.
This is a strange seeming experiment but it covers several things at once, and I'm disinclined to test 32 or 128 permutations if someone can say what the exact procedure is. I think that you (Joe) say that it's application-controlled. In that case, if someone has the rules for Office products that would be great!
And if you change the property but don't print, save file, reopen Excel - the change does not persist. Apparently with at least this product you must change the property and print (and possibly save File, and possibly restart Excel).
I'll let this die unresolved now and thank everyone who thought about an answer. I just wanted to give more data in case it helps someone else who finds the thread down the road.
(Since I don't see that I can edit post - last test was from selecting all sheets, then changing property without clicking "entire workbook")