Depending upon which programme one is using as a VPO the controller changes method is working for me as mentioned above. For different organs I save the definitions and combinations in each programme so that I can load them for a particular organ. That way it makes it easier to remember. So using whatever is available on a particular keyboard, such as unused keys, pads, knobs, sliders, mod wheels, etc. is much preferable to using the mouse for me.
I read yesterday that you can now purchase touch screen "overlays" for LCD monitors and it is way cheaper than touch screen monitors.
Since I have also finally gotten the free version of Hauptwerk to recognize my swell shoes and pistons, I can save combinations settings and assign them to available switches. As for individual stop pistons, I still have to resort to using the mouse. I guess I'll be making the plunge to a bona fide copy of Hauptwerk now that I can actualy get the pistons/couplers to work. Of course, after the initial investment for the software comes the even more expensive proposition of purchasing 3rd party samples for Hauptwerk. I'm toying with the idea of getting a part-time job in order to save for the samples I would like to have...they are all so expensive. But with using the GigaStudio Orchestra programme with the oran programmes, I'm starting to have a nice collection of organs thanks to Ebay.
So, for me it's Hauptwerk, Miditzer, GSO, Kontakt, MyOrgan, Reason, Toccata and Native Instruments. I've only played around with the stand alone versions until now. Next will be to start using my sequencer progs and see how that goes.