using Blender 2.5
This example will subtract a cylinder from the middle of a cube.
1. Position your object within the 2nd object, in this example the cylinder is moved into the cube.
2. First select the object you wish to Cut out, then use the Shift key to select both objects
3. Open the Modifiers property (looks like a wrench)
4. Click Add Modifier, select Boolean
5. Change the Operation to Difference
6. Select the Object to CUT out (the cylinder) from the Object drop down menu
7. Click the Apply button
8. It will appear as if nothing has happened. Select just the cylinder and move it
9. You can now delete the cylinder