I'm awfully late, I realize, but I like this solution from Make magazine for turning chits or counters into something that stands up. I didn't go the full shrinky-dink method, but I did use cardstock for the printed paper figures and binder clips for the bases as shown. No, it's not 3-D exactly, but they have more presence than counters that lie flat.
FYI Games Empire just moved over to Castle Hill (Grand opening on Saturday 21st). They also have the D&D books cheaper than Amazon, if you can drive over there.