I'm afraid to admit it, but I actually had a fairly positive polygraph experience.  It didn't HAVE to go this way, however.

I took a counterintelligence (CI) scope poly to get a TS/SCI clearance for a contracting firm, with the eventual customer being a US military agency.  (It's my understanding that the customer is the one who dictates clearance policy.)

As I read elsewhere, this test ended up being the standard TES (terrorism, espionage, sabotage) test that's described at  http://www.fas.org/sgp/othergov/polygraph/dodpi-tes.pdf . I had originally feared that it would be a presumed-lie format, but it ended up being the much easier directed-lie format.

As this is a narrowly-scoped test, I intended to (and did) answer every question truthfully.  However, word of mouth at my workplace indicated that most people take 2-3 sessions before they achieve sufficient "response".  It was easy to see why. I employed countermeasures because I wanted to get this over with as quickly as possible. I truly feel that anyone would have figured out these same "countermeasures" after two or three tries, however.

Maybe the difference between this and other experiences I've read is that in this case, a lot of money had already gone into my case and they wanted me to pass.

They didn't pull any of the tricks I've read about.  The office was a reasonable temperature, I wasn't kept waiting long before I went in, and during all the breaks between tests, the polygrapher let me get up and get a drink of water and sit back out in the waiting room for 5 minutes or so.

The whole process took about 3 hours from start to finish; I was strapped in the machine for about half of that, and actively monitored (well, had the pressure cuff inflated for about 20 minutes total).

I sat down in the chair and had the straps applied, the electrodes placed on my fingers, and the cuff put on (but not inflated).  The polygrapher gave his spiel about how it all worked -- standard stuff, although I found it interesting that he said "This is not a lie detector -- the only lie detector in the world is mom", and repeated that a few times...

I began maintaining a steady breathing pattern as soon as I was strapped in, and we went through the standard known numbers game -- I wrote a number on the paper and he wrote down other numbers, and asked me to lie and say no when asked if I wrote my number -- and he reassured me that I responded well. 

Then, he began on the first question set of three -- he spent what seemed like 15-20 minutes of explaining each question, defining it very narrowly.  Then he established the directed lie questions, which were, as I recall:

Have you ever violated a traffic law?

Have you ever done something that made someone angry at you?

Have you ever lost your temper at someone?

Have you ever bragged about yourself to impress others?

(There were two question for each of the three sections; I don't remember the other two.)

Other than that, the three sections went by smoothly and I would have expected.

I tried to employ the "pucker" CM but had little luck with it -- I can't seem to do that and at the same time maintain a normal breathing pattern.  I was called out for holding during one of the DLC questions.  After that, I just used a different breathing CM on each of the remaining DLC questions.

When I finished, the guy went out one last time and "consulted his manager", and came back and told me that it looked like everything went fine, although it would have to go through "three or four more levels of quality assurance"?  Strange.

Anyway,  it all came out fine.  Not that I'm saying that I think it had any validity; I just seemed to have lucked out.

If anyone else here will find themselves in the same situation, I'd be happy to answer any questions...