As I understand it, there's nothing to stop you using WHDLoad for that, although you'll possibly lose the multitasking.
(Can you do WHDLoad and still multitask? I've never noticed/seen that.)
I'm guessing what might be easier, is a universal installer pak kind of setup for each app.
Maybe a bit like the BTTR stuff.
(That wasn't app specific that I remember, but had paks of apps.)
Assuming most people use ClassicWB, you could probably do that without too much trouble. You could basically do a filesystem DIFF before/after an install which should work for everyone who has the basic structure (i.e. uses ClassicWB).
It does possible get iffy with things like app dependencies, but again, having ClassicWB as a base helps that...
desiv