The Computer Science/software site is called Stack Overflow. That has a natural meaning for that field. The more general site is called Stack Exchange. What does that refer to?
I believe since Stack Overflow was the first site in the exchange the 'Stack' just comes from there for familliarity/branding. Exchange as a suffix come comes from the generic term 'knowledge exchange', which Jason Calacanis explained to Joel and Jeff in Podcast #56, half a year before the launch of Stack Exchange 1.0.