The reason for using different pots is for different ranges of responce. Taking the bass pot as an example, on many amps the bass pot really only responds from 0 - 3 when using a 1M pot. So changing it to a 500k or 250k gives more fine control over the usable range. Depending on how it is wired (to the top of the mid pot or just a variable resitor to the tone cap), it can also change the bass curve of the tone stack.
A great tool to visually see what is going on is the Duncan Tone Stack Calculator which can be found at
http://www.duncanamps.com.