Using Miniatures
I buy many (I have hundreds from Ral Partha, Grenadier, TSR, Reaper--mostly Reaper now), paint a few. These generally represent the PCs.
I don't really like the pre-painted because I can only pick up random boxes and that seems like a waste of $$ to me.
I use counters I made. And some templates I made.
I use 48 vinyl, multi-colored, transparent ninja I bought from OrientalTrading.com for chump change (they sell now for less than $6). Then I mounted them on square bases--that cost more than the ninja themselves! Used a silver sharpie to give each base a number and swiped one side to be the front. Everybody
loves the ninja. Useful in any genre, perfect for Ninja Burger (their original purpose)!

I've stuck them into a large dice bag. They are light-weight, don't scratch, easy to pick up, drop, and face on the table, identifiable by color and weapon if you're not sitting on top of the map.