It would be best if you asked those questions in each of the product forum which you are inquiring about. I can move this thread to one of the forums. Do you have a preference on which specific application you would like to begin with?
Yes, please move it to the InDesign forum & I'll post another one in the Photoshop forum. Thanks for the advice.
Moving this discussion to the InDesign forum.
From the perspectiv of InDesign there is no set of preferences that is "best" other than the customizations you make for yourself to suit your won work habits. ID is still a 32-bit application and cannot use more than about 3 gigs of ram, but there are some things that will slow it down on some systems -- Live Preflight, cross-refernces and hyperlinks in documents, GREP styles, page previews in the Pages panel, Live Screen Drawing, High Quality Display performance, for example. I doubt these would present much of a problem on your system, though.
The photoshop folks will probably tell you to set your scratch disk to soomething other than the primary partition (a fast, dedicated, drive is best) and to set memory usage at 70% max. Setting the Illy scratch the same way would be a good idea, too.
Generally speaking, freezing and crashing problems don't have to do with performance configuration settings, and there are fairly few such settings that affect most applications. Video editing software tends to have a bunch, but that doesn't sound like it is pertinent to you.
Indeed, your hardware sounds far more powerful than you'd need to easily avoid problems based on performance limitations.
I suspect, then, that each of the problems you are seeing is a seperate unique problem not a result of a configuration choice. It'll need to be debugged carefully with full details, and as close as you can get to a reproducible case as possible.
In InDesign, about the only settings of relevance are whether Live Screen Drawing is turned on (images resize in realtime when you adjust their bounding boxes), and whether the View > Display Performance setting is set to Typical (the default) or High Quality.
You could also experiment with disabling Live Preflight.
You mention running 4 apps at once -- when you do so, are the non-active applications performing computation, or just sitting there idle? For instance, are you executing a complex filter operation in Photoshop at the same time as exporting a PDF in InDesign, all while you are drawing patterns in Illustrator? I assume the answer is Probably Not, in which case it lends strength to the hypothesis that the performance characteristics of your machine are not at issue here.