If you are talking about distance driving or distance shooting, and a shaft encoder doesn't do the trick for you, here are some options that my team has explored in the past in similar situations:
1) Try mating the encoder to a different part of your drive train.
On my teams robot, rather than attaching the encoder to the axle that supports the wheel, we used our encoder to count revolutions of a gear in our transmission.
2) Optical encoders.
Because the shaft doesn't turn with the wheel, measuring the shaft, as you pointed out, wouldn't help much. However, you can, for a slightly less accurate measurement, use an optical encoder and some reflective tape.
3) Trial and Error with timers
As noted, possible, but time consuming in the "lets-try-it-out" department. An option not to be discounted, but not what I'd take as my first route.
4) Hall-effect sensors.
FIRST does include hall-effect sensors, which can count gear teeth, but I've heard mixed results about their implementation.

If you are trying to calculate driving distance, you only need the encoder and a known starting position (use a 3-position switch to accommodate for each starting box). Also, keep in mind that in their most simple implementation, these sensors act as courters; they are independent of direction. Hope this helps.

-Mike, Team 341