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Generally speaking using the "high quality" settings are quite sufficient for all your work. It is essentially the same as the PDF/X-1a settings but:
Fonts that can't be embedded are allowed
Conversion of colors doesn't happen
PDF/X-1a or PDF/X-3 metadata keys aren't added
The problem with the PDF/X-1a:200x settings as provided by Adobe is that in order to make a file PDF/X-1a compliant it must be converted to CMYK. By default Adobe uses the SWOP profile. Which most people print some form of SWOP on coated or uncoated anyways. Quark if I recall correctly doesn't give you the option of making a PDF/X-1a:200x directly.
For Adobe apps you can't really make a 1, 2 4(CMYK) or 4+ PDF export setting. You either leave color alone or you convert to a color space. So that's real easy. With Quark you have a number of choices that each have their own side-effects.
I would submit that for Adobe apps you need:
Spot (and cmyk) this would be your catch-all setting
CMYK Coated - the coated profile could be what ever you want it.
CMYK Uncoated - same as above but for uncoated.
For Quark it would basically be the same thing.
Then in the settings I'd define 9pts of bleed, 9pt or 12pt offset for the marks
crop marks, page information, ZIP compression, no downsampling, "high resolution" transparency flattener, PDF v1.3. If you want to preserve transparency then make a new set for un/coated, PDF v1.5 and transparency will automatically be preserved (again, thank you adobe....)
Printers that don't need the page marks or info then can place the PDF by the bleed box which will have the net effect of ignoring the crop marks (remember the 12pt offset?). Those who do want the marks will place by the media box. Those that use automated imposition like Preps usually have Preps or the imposition program of choice set to use the trim box. Even if it is set to use the media box the content will still be centered in the imposition. Now with CS3 all the Adobe apps share the same common .joboptions file. It was like that in CS and CS2 to a certain degree but the settings were stored in separate places because of how the application specific settings were stored in the joboptions file itself.
And it wouldn't be such a bad thing to pass spot colors, tagged RGB or tagged CMYK to your printers so that they can do the conversion for you. That would make things much simpler on the export side. But then it would add a layer of complexity to the proofing stage(s) (and hopefully there's only one stage). Providing RGB also allows for a more flexible workflow on the back end for you amongst other things.
But generally speaking the "high quality" settings will get you 9/10ths of the way there right out of the box.
Look to PDF/X-4 and PDF/X-5...
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