Besides a HUGE collection of metal & plastic minis, cardboard pieces and Steve Jackson standees, I’ve used dice, checkers, tiddlywinks, glass planter/game beads, jelly beans and other things. My favorite, though, happened because of a scrivener’s error.
Since I’m usually the host on game night, I’m usually the game piece supplier for several of the other players & GMs. One of the guys in our group was playing a stereotypical human paladin in heavy armor with a sword & shield in a 3.5Ed game. On his character’s sheet, he described the paladin as 6’5” tall and 135lbs. So I gave him a needle which I had stuck into a cork.
As hilarious as we ALL found this, it actually was kind of inspirational. In a subsequent 4Ed campaign, I played a Starlock/Psion who had all kinds of ephemeral effects I had to track- some spells, some little “motes” and even some summoned/created entities. Unlike a similarly designed 3.5Ed PC, there were no variations in what was created. So instead of using dice, etc., I used the same needle & cork idea. However, I pushed the needles through different, distinctive beads, then into hard styrofoam craft plugs so I could tell them apart.
So for one spell that created twinkling motes of force, each mote was represented by a needle covered by tiny, faceted clear and icy blue beads which sparkled. For another effect, the beads were larger and red. And so forth.
But now I have switched to proxy terrain 
