Chipotles (smoked jalapenos) are one of the best pieces of gear in a cook's arsenal. With them, you can deliver smokey heat with an undertone of pepper flavor, all in one spice. Unfortunately, your off-the-shelf options are chipotles in adobo sauce (good, but only if you are making something complimented by adobo sauce...), or really expensive spice jars.
If you have a smoker, however, you're a couple of dollars away from a superior spice that keeps forever in whole form, ready to be ground into powder or dropped whole into soups, stir-fries or braises. If you reconstitute a couple of them for an hour in warm chicken stock, you have a great base for tortilla soup. Powdered, they go into everything from taco filling to chili.
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Step 1: Smoke!
Start with however many peppers fill up your smoker. I use a pound per shelf roughly (this batch included two poblano peppers that needed to be used up). If you want a sweeter pepper, use fully ripe (red) jalapenos. I prefer the green.
Set your smoker to 190 degrees F (88 C). While it comes up to temperature, soak your choice of hardwood chips (I like hickory and mesquite) in water.
This is an 18-24 hour process. I structure it so that I tend the smoker for the first 12-14 hours, then I add a bunch of wood and just let it sit overnight. If you don't want to leave your smoker going all night, transfer them to a sheet pan in an oven set to 190 degrees as well and let them dry in it overnight. They probably not absorbing a lot of flavor during the last 8 hours of the process anyway -- you're just getting rid of the last of the moisture.
Important: Do *not* let your smoker (or oven) get above 200 degrees. You do not want to *cook* the peppers, you want to *dry* the peppers.
The peppers are done when they've lost all their moisture.