Here's a recipe for adobo sauce that I use when my smoked & dried Jalapenos are crying for attention. I've adapted it from Mark Miller's recipe in The Great Chile Book. With the mass quantities of green tomatoes ripening in boxes in the basement, I've substituted them for ketchup. Seems like a good change.
The chipotles are sort of my adaptation. If anybody has any other ways of making them, I'm all ears. I take the fresh Jalapeno chiles - generally the ones that have ripened to red and smoke them in my old charcoal grill with some Mesquite wood chips that have been soaked in water for a couple of days. I put them in a makeshift wire basket that I put on top of about 4 or 5 charcoal briquettes (don't want things to get too hot). On the grate above, I load up with chiles, with the exception of the area right over the fire. I let these smoke as long as my patience holds out (maybe 4-5 hours), occasionally turning the chiles and tossing a little water on the glowing wood (want it to keep the works smoking). When the chiles seem soft & kind of cooked, I put them in a dehydrator to finish the job. They're then stashed in a big jar, etc. Until I'm ready to use them.
The sauce isn't too complicated to put together.....
Peel and cut the onions into half inch slices. Peel and slice the garlic. Toast the oregano and cumin, but the cumin needs your almost undivided attention. It will burn in a heartbeat. I usually wait until it just starts to smoke. I think I've burnt more cumin than I've toasted! All this stuff goes into a 3 quart saucepan (or larger). Cut the tomatoes into quarters and grate them on a regular cheese grater down to the skin. Discard the skins. Do enough tomatoes to make 6 cups - a little more is Ok, I'm sure. The mash should be fairly watery - add some water now if you think it needs it (some store tomatoes are sort of dry and pulpy). Put the vinegar, the salt and the tomatoes into the saucepan. Slowly simmer this mixture for about 3 hours, stirring occasionally. Somewhere in the middle of this stewing process, put in the chipotles to rehydrate. By the end, they should be nice and plump, with their smoky flavor well mixed with the sauce. The sauce should want to coat a wooden spoon.
After everything cools down a bit, fish out the chipotles, leaving in a few to spice the sauce to taste. Puree the mix well. I find that the sauce seems thicker when it's pureed, so that now a metal spoon is coated when dipped (that happens often, now!). At this point, you can decide whether to strain out the seeds, etc. Or not. I go back and forth about this, but usually don't. Anyway, put whatever you decide on into a container with the rest of the hydrated chiles. Whenever you want a chipotle, you know where it is and the sauce keeps for a good long time in the fridge.
I use it whenever a good hot smoky flavor seems to fit - steak or chicken sauce, as an ingredient in another salsa, ...........