Pick up a ship from Star Wars X-Wing and it comes with about six different token types. Or, ask an X-Wing player if they can spare a couple tokens of various types. Since I play 40k at a LGS, I just picked up some tokens from there and made it work and now that I play X-Wing as my main game, I have more tokens than I know what to do with.
The best solution I've seen though is little dry erase tokens. Mark it with a letter, erase it when the effect is over. Let's you use the same tokens for a whole bunch of effects with very little chance of getting them confused.