I just throw mine away right after using them. Of course I always take the whole $500 off, and when I have $421 cards I try to use them right away, to avoid the chance that I spend $421 with a $500 card and then throw it away.
I don't keep a precise log of cards and such, but I do count them each time, and I'm careful to put them in the place they belong.
In the years I've been doing this and $1 million+ of GC's, I've never had anything happen that made me feel I'd left money on a card.
I sometimes wonder if anyone tries to rescue my cards from the trash can at the exit or on the restroom at WM and see if there's anything on them.
I feel more comfortable throwing them away than wondering "Have I actually used this card?"