Have you considered numbering your CF cards? That way you should be able to remember which you have used - particularly if you use them in order. Personally, I used to put empty ones in one ziploc bag and filled ones in another.
Personally, my Compact Flash cards are numbered, and I cycle through them in order. I am never confused about which ones have been used and which ones have not.
I only have 7 and I can count that far, when I get to 7, I go back to 1.
I always know which ones I need to download to my final storage location, and which ones are still empty.
Numbers are an elegant application here.
I also have one of those mylar address stickers with my info on the back of each of my cards, and my first name in large letters on the front.
My 7 Compact Flash cards are roughly the size of the USB cable and a change of batteries required for one of these hardrive based temporary storage solutions. And as a rough guess, slighly lighter than the cable and change of batteries.