The general rule of thumb is that audio taper is used for volume and anything approximating the volume-like function, where linear is used whenever knowing the "middle" of something is important. As you might expect, linear pots are used for things like blend/mix/balance controls, as well as for EQ controls where identifying exactly where you are either boosting or cutting is important.
Beyond that, my experience is that it would depend on your needs. Some folks want all the control at one end of the range, some want it at the other, where others want equivalent "dialability" over the entire range of control for that pot. For instance, say an LFO for a flanger goes from .1hz (one sweep every 10 seconds) to 5hz (5 sweeps per second). One player may want to be able to dial in subtle differences between .1 and .5hz, where another may be far more interested in the range between .7 and 3hz. What makes for more "dialability" for the one player may be exasperatingly restrictive for the other. And THAT is the essence of pot taper; you go with the taper that allows you to easily replicate settings you are interested in. In some instances, that might be linear, in others audio/log, and in others it may be reverse audio/log.
My own inclinations lately have been to use a bidirectional tone pot, where I treat a single 1meg linear pot as two parallel tone controls, each with a different kind of rolloff. In one direction it cuts at one frequency, in the other it cuts at a different frequency, and in the middle it doesn't cut at all. Because I have essentially taken the rotation of each virtual control and cut the amout of rotation needed in half, it really doesn't matter what the taper is because with such a reduced range of rotation, you don't have the sense of portions of the rotation as being "useless" - i.e., you notice an effect no matter which way you turn or how much.
For folks who like a traditional sort of tone control, though, you can wire up either a lin or log pot and it'll work just fine. If you want to be able to dial in small differences in mutedness, you may want to go with log or reverse log. If you feel more at ease knowing that you really need to roll back the tone control before you start losing treble, then linear is likely better.