Here's what I've been doing lately-
I've been experimenting with smoking peppers as well. I'm of the opinion that damn near every food should be smoked, grilled, pickled, or canned- or any and all of the above. You can just smoke the peppers and use them in whatever salsa recipe you already have to make a chipotle salsa- vary your smoke to vary the amount of flavor you want. What I've been honing in on lately is a form of Salsa Borracha (drunken salsa)- basically, I smoke the hell out of the peppers, half of them I leave whole and the other half I halve (that sounds confusing!). I smoke those for three or four days until the halves are completely and totally dehydrated- the whole peppers are still somewhat hydrated. This is a cold smoke, so they don't cook, they dehydrate. Once smoked, I rough-grind the halved peppers (just run a rolling pin over them until they are broken up into coarse chunks) and put all of the peppers and other ingredients into a saucepan filled with beer on low heat, and let them reconstitute in the beer. Once that's done, make your salsa.
Peppers, beer and smoke- how can you go wrong?
