I often do while using my spot meter is meter a scene, then hold the filter up and and re-meter the scene, using the exact same reference points. While 3 stops is the calculated average, depending on subject matter and lighting conditions, I have sometimes used between 1.5 to 4 stops for the same filter. If in a hurry, I use 2.5 stops; if you are using a camera with TTL metering, the camera will compensate for you.
The other thing to remember is that filters do not always work equally on all areas of the a photograph - if I am taking a picture with trees against the sky and put a red filter in front of the camera, the filter will darken the sky 3 stops. However, the shade under the trees is more blue than the sky: the sky has a blue background but is lit by sunlight, which consists of a number of colours whereas the shade is lighted only by the reflection off of the blue sky (and not the sunlight) and thus has less colours in it. As such, the shade might be darkened by 3.5-4 stops; this is important when placing shadow values.