This page will assist you in calculating where to place holes in a PVC pipe flute, whistle, or recorder. The calculations will be correct for any type of mouthpiece, since they are based on your measurement of what the base note of the instrument is. The calculator on this page assumes that you will make all your holes the same size, and that they are round.
Hole acoustic length:
Hole Distance from End (cm)
The numbers given in the table above under "Hole Distance from End" are how far you should measure, in centimeters, from the open end (not the mouthpiece end) of your whistle, to the center of the hole. The hole can be rotated to any position around the pipe, as long as it is at that distance; you may want to move some holes a bit off center to make them easier to reach.
If you'd like a full explanation of the physics behind this, look at "Physics of Musical Instruments" here.