Separately from the fact that I don't think $400 gets as much benefit as you seem to, I don't think the idea that you would be willing to pay $400 to avoid a nephrectomy is a good reason not to donate a kidney, at least without the additional stipulation that you're not willing to donate $400 more. Imagine a case where an individual believes that donating a kidney is worthwhile for benefits to others, but that they would happily pay $400 to not undergo the surgery (this may be your case, I think it would be mine, too). He pays the $400, and then face the question again. He still has both kidneys, can still benefit someone else by the same amount as before, but he has $400 less, so then he decides again whether to donate a kidney or donate $400. (...induction...) Eventually, he either donates a kidney or decides that enough has been asked of him. Another, perhaps more straightforward, way to put this is to say that the fact that there's some amount of money that achieves equivalent benefit to donating a kidney only tells you not to donate a kidney if you're sure you're not willing to give more money; the implication could just as easily be that you need to give a lot more money. I'm actually not sure what the amount of money (i.e. the $400) has to do with it in your framework, since for any given amount of money the repeated question means that you eventually reach your limit in willingness to pay to avoid surgery.
If the opportunity cost of donating a kidney is $400, because of the opportunity costs of not being productive during the surgery and recovery, then you are effectively donating $400 in addition to your kidney to the cause of giving someone else a kidney. It seems reasonable that the $400 would come out of your charity budget, and you should consider if another charitable cause could use it more effectively.
Just to be clear, I think that in jkaufman's argument, the $400 is not the opportunity cost of undergoing surgery, but rather an estimate of the amount of money AMF would require to achieve comparable benefit as donating a kidney.
I agree that if you had to forego income during surgery or incur other costs, then it would be reasonable to add those onto the other side of the ledger as you propose. As I mentioned above, though, I think that's typically not the case; medical leave policies are often quite generous in these cases, and public funds are available for incurred costs.
People are dying because their kidneys have failed, and you probably have an extra one: should you donate it? A dialysis machine can do most of the work of a kidney, but it's not as good. A donated kidney gives someone an average of 10 additional years. [1] (Some of them reject it right away, others live for years before having problems.) This is pretty good: if you volunteer to be a kidney donor and are selected as a match, you give someone an average of another 10 years of life. [2]
A kidney donation is a surgery, however, and does have some risk for you. It's hard to calculate the risk because people who are selected for kidney donation are a weird group: they're heavily screened (so they tend to be healthier) but they're likely to be related to the person they're donating to (so they tend to be at risk for kidney problems themself). An ideal study on the dangers of kidney donation would compare donors with people who were going to donate and then didn't for some nearly-random reason. I can't find such a study, but I've heard people give odds of around 1:3000 for dying due to donating. You also spend several days in the hospital, miss some weeks of work, and take several months to fully recover. [3] This sounds like a lot, but giving someone 10 years of life is a lot too.
The question isn't so much "does this do good," however, but "does this maximize the good I can do for the amount of sacrifice I'm willing to accept?" GiveWell estimates that each $1600 given to the AMF for antimalarial net distribution prevents the death of someone with an average life expectancy of maybe 40 years [4]. So another way to give a stranger 10 more years of life is to give $400 to the AMF. Kidney donation is in the same ballpark as this, in terms of the ratio of benefit (to others) to cost (to you) [5], but even ignoring the risk of death [6] I would pay that $400 just to avoid the hospital and recovery time.
Update 2012-06-22: BDan and Alexander Berger have convinced me I was wrong to write off chains. At least right now there are more possible chains than kidneys to start them, and they can be quite long. My updated estimate is that this gets you a 3x multiplier on the value of a donated kidney, bringing the $400 charity equivalent to $1200. Which is still less than the $10-$100K at which I think I would sell a kidney, but substantially higher.
(I also posted this on my blog)
[1] Comparison of mortality in all patients on dialysis, patients on dialysis awaiting transplantation, and recipients of a first cadaveric transplant. (1999), table 3. This is from a longitudinal study on 23,275 people who got kidney transplants from cadavers and had never had one before. In our case we're interested in live donation, but I would guess it's about the same.
[2] It's possible that you could do better than this if your donation to a stranger set off a chain of donations. The idea is that there are lots of people who would give their kidney to a friend of family member if they could, but are for whatever reason incompatible. You can make donor-donee-donor-donee chains where it just takes one altruistic person to set the whole thing off. (Cycles are also possible, but they don't need someone to get them started.) The question is, though, how likely are these chains to happen anyway? And how long a chain can you reasonably expect? My understanding is that these are quite rare, with most altruistic kidney donors not starting one. I'm going to ignore chains.
[3] Someone who gave their kidney wrote in a Guardian article: "I was in hospital for four days--the worst part of the whole ordeal was removing the catheter. In just two weeks I was back at work (the full recovery is supposed to be three months)."
[4] I would love to find a GiveWell estimate of what life expectancy for the people who don't die of malaria because of a net, but I can't find one. So this "40 years" is a guess after looking at life expectancies for different ages in the countries where the AMF works.
[5] There are huge costs to both dialysis and kidney transplant, so as a health intervention distributing antimalarial nets [makes much more sense]. From the perspective of a prospective donor, however, I don't think this matters.
[6] You might think that if you're someone who gives a substantial fraction of their earnings to effective charity, a 1:3000 risk of death would be pretty bad because you'd be able to help other people much less. But 3000 is really big: if you're giving $20K/year and have an expected additional 30 years of working life, a 1:3000 chance of not being able to do that has an undiscounted expected value of only $200 less donated. [7]
[7] $20K * 30 years * 1:3000 = $200