Harsh thread. But I'm with the OP on this one (at least with respect to the perspective -- not NECESSARILY his situation), and unlike him, I don't have an axe to grind.
I ran into the exact same issue late this past summer, about 2 months after I had bought my 3GS. I'm the sole owner, and there aren't any kids around, so I am 100% certain I know where the phone had and hadn't been. And I'm 100% certain it never got drenched, soaked, etc.
Like the OP, I was stunned when the Genius said the moisture sensor had been tripped. He said it was "pinker" than most he sees, indicating that the moisture exposure was less than many, but that it was still clearly tripped. And he lent me the tool (basically a light + magnifying glass) he used to see the sensor, so I could see for myself.
I was sort of dumbfounded with the guy. Basically, I said, "Yeah I don't know what to say. I can swear to you that I didn't get this thing wet, but I bet you get a lot of people who come in here every day who know damn well they did and just want a free replacement." I can't even describe the sort of sinking feeling you get knowing you have a legitimate complaint in an area where so many other people don't, but it's a feeling of helplessness. I felt worse because, as this was my first iPhone, I'd babied it. I refused to use it until I got a case and screen protector, I'd always carried it gingerly, and the couple times I had to carry it in the rain, I bent myself over like a hunchback to protect it from the prospect of any water getting on it.
Like the OP, my problem was clearly not one that water damage ever would have caused. I had intermittent issues with people understanding me. Sometimes calls would be crystal clear, and others they would be garbled. It had been like this since day 1 of having the iPhone, and I simply hadn't gotten around to replacing it because I don't use it as a phone very much. (Learned my lesson!)
Well, bottom line, I called Apple Support and spoke with a guy there. I explained the situation, explained I was 100% sure that it wasn't water damage, and he told me that if I sent it in, they'd investigate my claim. If they concluded that it had water damage (regardless of whether that was the cause of my issue or not), they'd charge me $199 -- if it didn't, then it would be a warranty replacement. I happily took him up on this, and bought AppleCare over the phone (since that enabled me to get free shipping to Apple).
Well, turns out this fellow was wrong. That is *NOT* Apple policy. When you send it in, they just look at the sensor too. There is no effort to determine whether the unit has "damage" or not -- they don't even open it up right then and there. After another couple calls to Apple, I got a supervisor to make it right (because the conversation notes were right there in my case file and I'd been clearly misinformed), but it was an ordeal.
The Genius I talked to said that he's heard of condensation from cupholders in cars possibly tripping the sensor, but as I told him, I don't put my iPhone in a cupholder. He also said that a group of Geniuses had tried to see what trips the sensor, and that they'd taken a phone (I assume a busted one) and dunked it in water until it turned, and that it took 30 seconds. As a result, they concluded that the sensor doesn't get tripped very easily at all.
I have a theory, though, and this may be relevant to the OP: humidity. Do you live in a very humid climate? Or, more important, have you taken your iPhone with you into the bathroom when taking a shower? I had taken mine in a couple times (to answer business calls if it rang) with my old one, and I'd kept it out with me on vacation while at the beach (but never getting it wet). I haven't done either of these things with my new one, and its moisture sensor hasn't been tripped. I don't exactly wanna test my theory on my phone.
But I have read people online complaining that they think humidity is the cause too.
Anyway, TLDR: I am sure there are people who aren't trying to pull a fast one, because I was one of them. I guess I got luckier than most. It's a damn shame Apple puts these sensors in *externally accessible* areas as opposed to more internal ones (like behind the batteries, as is the case with more cell phones), although it's obvious why they have to do so with the iPhone device. Still, I'm sympathetic to those who have not damaged their device and are SOL.