This word is associated, in my mind at least, with exploitation of workers and bad environmental conditions. Many American companies locate their factories just across the Mexican border in order to take advantage of cheap labor and less restrictive environmental regulations.
A couple of thoughts on this (largely not word-related, but perhaps of interest):
I work for the US Environmental Protection Agency on hazardous waste issues on the US-Mexico border - in short, I work on the nasty crap that maquiladoras produce. In general, I'd have to agree with Rapunzel's characterization of the maquiladora industry, although I believe the labor costs are a much greater factor in companies' relocating than the environmental regulation. Mexico actually has pretty stringent environmental regulations - they just lack the resources to enforce them. Mexico also has very strong labor regulations - they just lack the will and the resources to enforce them.
Also, there are numerous exceptions to the stereotype of companies polluting madly upon arriving in Mexico, as many of the largest companies simply have the same environmental operations the world over. But the smaller, mom-and-pop shops, and the Mexican companies that often provide parts to the maquiladoras, are largely unregulated.
I've heard a number of other theories on the etymology of this word, but haven't any of them handy.
Some random factoids about the maquila (this shortened form is used as often as the full word) industry:
2/3 of the televisions bought today in the US are manufactured in maquiladoras in Tijuana.
In 1994, there were about 2000 maquilas in all of Mexico (about 80% are along the border). In 2000, there were over 3500. That's 1500 new factories in 6 years - growth unlike any I've ever heard of.
In the last 5 years, almost 250 maquiladoras were built in Tijuana - that's a new factory every week in one city alone - the highest index of industrial growth in the world (and, perhaps, in history).
In that same period, the number of environmental inspectors in Tijuana has remained the same - about 4.