Smoke whole jalapenos for 45 minutes at 225 F using mesquite wood chips and shavings.
Let peppers cool until you can handle them. Remove seeds and slice into strips. Pack into a pint sized canning jar alternating peppers and onion slices.
Mix together the vinegar, water, and brown sugar. Pour over jalapenos in jar. Let sit in the fridge for about a week. Serve on sandwiches, pasta, polenta, burritos, or tacos.