I think you got it all wrong. The crop marks effect is just that - an effect that creates some renderable objects for output. it never was any different. If you are referring to the former crop tool, then that is now artboards and the optionjs to use them must be ticked in whatever exporters and savers you use. Still, for web output it's not really the most efficient method, you would do that with slices, which can exist without affecting your initial art. But they are already in CS3, so I'm wondering why you nbever used that method in teh first place...
In CS3, I would create a square shape around the image I want to Save For Web. I would select the Crop tool, set it to Object and it would create the crop around my selected object. When I Saved For Web, it would only save the artwork within the crop marks. Now in CS5 I seem to have to do extra steps to get it to do the same thing. I have to make my square, turn that square into the artboard, the Save For Web and check the Clip to Artboard under image size. When I'm done, I go back to the art work and Undo until the artboard is back to my working size. Not very convenient with my work. I use Save for Web all the time to save pngs with transparent backgrounds, either as single files or as layers for animations.
You do speak the truth so in CS 4 and now Cs 5 you instead of drawing a rectangle and the making it into crop marks you simply draw an artboard then when you export you select to use artboards in the export dialog and select the artboard you just made and voilá.
Now before you go crazy this is an advance you can also choose to export all the artboards a range of artboards or a non-contiguous selection of artboards this way.
the difference here is that you draw the artborad which is actually drawing a rectangle and making the crop marks as in the CS 3 all in one opertation
it is really the same feature with lots of features added to it. Including the ability to name the art boards (cropped areas) number them reorder them
manage them in the artboard panel and then the team went farther than that with pasting in place pasting an element on all the artboards at once.
It is really just the crop area feature but with lots of possibilities.
If you need t draw an artboard within another artboard hold down the shift key.