#1 What are the best ROM files to use with WinUAE? Where can I get them? As far as I am concerned I already own over a hundred ROMS, and I can't see why me having other software versions of those ROMS could be against any laws/rules -- now I'd like the very best sets for my emulator thank you very much.
I have two ROM images handy: 1.3 and 3.1, to reflect my A500 and A1200. I've not had any compatibility issues.
#2 What configuration would you say is the most stable and functional to use?
I think you'd be better off asking more specific questions as to configuration :-) It depends on so many things, and I tweak configs for some games.
#2b What hardware setup is thought to be the be the "best" for stablity? I intend to use this on a P4 3.2GHz 1GB 800MHz RAM, GeForce 3Ti500 machine currently running XP Pro - should I change the video card or OS or anything? Any tips here (I don't care about the cost, I have a pile of PC hardware to try swapping around if there is some optimal setup to be had...). I'm mainly after a stable games playing environment all running on one box (it already runs MAME with ~3000 roms for example).
No, you only need a DirectX-capable card, nothing fancy. Pretty much, only one thing really matters with Amiga emulation, CPU. Lots of it, and good at both integer and FPU.
#3 Are there any good sources for ADFs other than back2roots.org?
Yes. Google is your friend.