KishKish
has released a Skype add-on that does voice stress
analysis (VSA) (þ ITwire).
The American Polygraph
Association (not exactly an unbiased source) claims that VSA
doesn't work, but let's say it does work. How hard is it to counteract?
The high-tech way is to build a filter that removes the signal
that the analyzer on the other end is looking for. This probably
isn't that hard, especially since the developers of the filter can
use a local copy of the analyzer as an oracle to figure out
whether they've got it right or not.
The low-tech way to do this is to run a local copy of the voice
stress analyzer and use it as a biofeedback monitor to detect
when the analyzer on the other end would think you were lying.
Of course, if you're dealing with someone who is
running voice stress analysis on your phone call, you might
consider finding new people to talk to.

My guess is that a) this is pretty much snake-oil and b) even if it isn't, the highly variable latency quality of calls across an ad-hoc semi-P2P VoIP network like Skype, while tolerable to human ears, produce a ton of false positives as well as 'stress detection' failures.