I am collecting Don Mattingly cards from his playing years only. Luckily he stopped playing before they started coming out with the volume of crazy parallels and inserts you're referring to. So, the checklist is pretty well defined and there aren't that many cards that are truly scarce. You could find players who finished their career around the same time (mid 90s) or earlier if you are looking to attempt a complete collection.
Right now my collection is stored in a couple binders, plus the more expensive cards, oddball sized cards, or special complete sets (like the Star series of sets) sized stored separately in a plastic tub. These cards I would still keep out of the binders even when I get things organized, but I'm not sure how I would want to 'present' these in the binders with placeholders, if at all. I do like the idea you mentioned of having a small photo of a card on the placeholder, but I'm not sure I would do that for everything because of the amount I'd have to print out.
