Well, I've got some of those 9 card sheet protectors (I used them back in the days when I was playing M:tG) and my players have been using them to organize their magic items.
"If you don't have the card, you don't have the item..."
It occurred to me today that I could use these same sheets to organize a dungeon made of geomorphs!
My first attempt involved using Goodman Games DCC #9 Dungeon Geomorphs -- here they are in their sheet.
You can buy the PDF file over at Paizo and when you print it, scale it to 78% (that's approximately 2.5" x 3.5") These geomorphs are already rectangular, so they fit nicely in the pockets at this size. I recommend using cardstock; the thin paper is sometimes hard to slip into the pockets.
If you are using geomorphs from Risus Monkey or Dyson Logos, you can always take their images and drag them into a Word (or similar) doc. From there you can resize them to the appropriate size.
I think that building a dungeon in this manner might make it easier to make changes. If your dungeon is a mythic underworld, just swap out a geomorph or two each time the party enters. You can also rotate them 108° easily to confuse parties of adventurers.