A couple of papers discussed here and here (among other places: the chili pepper story in particular has been getting a lot of media coverage) describe how the minute, species-characteristic starch grains found in micro-crevices on stone tools and cooking utensils recovered from archaelogical sites are being used to study the domestication of crops as varied as maize, cassava and chilies in the Americas. The findings are pushing back the timing of domestication and suggesting that wet lowland areas were more important in the process than previously thought. Jeremy blogs on the chili angle at greater length here. No word on the past of cactus cultivation, at least in these papers, but this piece suggests its future may be troubled.
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