Source of smoky flavor in salsa?

Chipotle chiles, especially in adobo sauce (e.g., here), give an excellent smoky flavor. You should be able to find these in your grocery store in the Mexican section.

It depends on what sort of a smoky flavor you're looking for.

I've used chipotle peppers before, but you can also grill the peppers, onions and even tomatoes to get some char on them before chopping them up. (well, the onions I slice before roasting or grilling, then dice them afterwards).

Don't forget cumin! Cumin imparts an earthy smoky flavor.

One of my favorite store bought salsas is Trader Joe's Double Roasted Salsa. If I were stranded on a desert island, an endless supply of this would be one of my must-haves. It uses double roasted anaheim peppers and cumin to achieve it's amazing flavor.

Here's the ingredient list:

Tomatoes, water, double roasted anaheim peppers, onions, cilantro, cider vinegar, jalapenos, lime juice, sea salt, garlic, cumin, black pepper.

I haven't tried my hand at duplicating this, but I bet it'd be fun to try. Double roasting a pepper consists of fire roasting it, peeling, and fire roasting again.

If you do experiment with fire roasting tomatoes as Joe has suggested, save yourself some trouble and use Roma tomatoes. If you try using regular slicing tomatoes they'll just disintgrate. Roma's are sturdy, and taste great.

Regarding your equipment, I don't think you need a smoker for salsa. I've never had a salsa that had anything smoked in it that I'm aware of. The smoky flavor has always come from either peppers or tomatoes being fire roasted. You can fire roast things on your charcoal grill, but you can do it even simpler with your broiler, or even simplest directly on a gas stove burner. I would avoid the liquid smoke until you've tried a salsa with fire roasted chilis and/or tomatoes, chances are you won't need it.

You could try to add a teaspoon or two of smoked paprika. That gives a good smoky depth to the flavour, without being overbearing.

Not the classic answer perhaps, but definitely my fusion/experimental idea.

Chipotle chiles in adobo sauce are the most likely source. Most people don't use a whole can at once so when you open it, use what you need and then set the remaining peppers on a parchment/waxed paper lined baking tray and freeze them individually. Once frozen, pop them in to a zip-top bag so you can retrieve one or two as needed in the future. Save the Adobo sauce as well and freeze it separately to add to chili, stews, soup, or rice.

Chipotle powder can also be found in some spice stores. Chipotle powder and smoked paprika (available in sweet, mild, and hot) are nice because they give you flexibility for multiple uses...add as a seasoning to the salsa or mix with other spices to use as a rub on meat.

Additionally, you can also smoke some of the vegetables themselves...tomatoes, peppers, corn. This can be done on the grill with a smoker box, wood chips strews on the coals of a charcoal grill, or by other means.

I too like a smokey flavor in my salsa but I'm a total wimp. I can't do chipotle chiles in adobo sauce or even just deseeded jalapenos. I found Dash Southwest seasoning at Walmart and it's my go-to for my salsa. Between it and cumin I get that smokey flavor I like. I don't like cooked salsa, only fresh.