Once you smoke a jalapeno popper, you will never grill one again. The flavor is outrageous, and the bacon doesn't burn like it tends to on a grill, and in addition, the cheese stays inside and doesn't ooze out like it does when grilling. Choose your favor wood and get smoking.
Cut tops off of jalapenos, and using the end of a spoon or fork, stick down inside and rotate the fork. This will loosen the membranes and seeds, then dump them out. Do this a couple times if needed.
UPDATED 12/2013: Slice off a pc. of pepper longways, stuff, wrap in bacon and smoke. I find this way easier!
Place cream cheese in mixing bowl and turn mixer on. Grate 8 oz of cheese then add to cream cheese, beat for a minute or so.
Put cheese/cream cheese mixture into jalapeno and push down inside with finger. Tear a small piece of bread off, I like using the heal of the bread, and place inside the top of jalapeno, this will help keep the cheese inside the pepper.
Wrap pepper with bacon, starting by draping one end of bacon over opening of pepper. Then bring bacon down to tip of pepper and begin wrapping it back up to the top. Secure with toothpick.
Smoke on smoker at about 200-250° for about 1- 1/2 hr. Timing will depend on smoker temp. Best way to tell if they are done, make a couple more than you need to serve and test one out after one hour.