Most of the time I've seen this done with those individuals who collect raw cards and store them in pages/binders, is they make a high quality, double sided copy of the card, trim it down to size, and slip the copy into the binder page.
You could do this even if your cards are graded and entombed in plastic. Scan, print and trim a copy of the card, as many as you need for your various sets and subsets, and place the copy into a card sleeve and now you have a replica to look at as you shuffle through your cards.
Taking your Cobb example, you could keep the actual Cobb card itself in the T206 set, while having a copy/duplicate version in your HOF subset and another in your Cobb subset.
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