I have left unused tokens unpunched since the Core Set and Waves I and II and III, since that is when I got into XWing! Leaving them unpunched and in a box keeps them convenient and in "new" condition until I need them!
I hardly punch things out with each new wave, ship bases, mines, bombs, etc is about it. i couldnt tell you the last time I punched out a TL, Shield, Ion, Evade, etc.