I pretty much use whole hops exclusively; however, then again, I also use a false bottom in my kettle. Whole cones, a false bottom, and an immersion chiller allow one to drain clear wort from one's kettle. Whirlpooling helps to reduce, but does not completely eliminate hop material from entering one's fermentation vessel when using a ball valve-equipped kettle. A good compromise that I have seen used in several craft breweries involves using pellets in the boil and whole cones in a hop back while casting out the wort.