A bit of an update, September 3, 2006:
There is now an increasing amount of data to support both the traditional claim that circumcision carries substantial health benefits, and the more recent one that FGM is an unnecessary and dangerous procedure. It has been demonstrated by studies carried out in African and Western populations, that circumcised men are 60% less likely to contract HIV from a female infected partner (this is due to the fragility of the foreskin and its tendency to develop minute tears that allow for blood contact). This is a protection rate that easily matches those hoped for from any near-future vaccine.
In contrast, women who have undergone FMG are 55% more likely to give birth to dead or fatally vulnerable babies, on top of all the other well known risks to their own health (like an almost 70% higher chance of dying in childbirth, which in communities already weakened by HIV and poverty is endangering the baby as well, of course).
FMG is an abhorrent practice to Western eyes; but this is not why we should be in favour of abolishing it. Rather than waste time on academic disputes about relativism, cultural imperialism, Judaism and whatnot, let's just look at the facts and recognise that it is putting at increased risk a population which is already among, if not the, most vulnerable in the world.
A good article summarising the above data, as well as the histrionic excesses of the anti-circumcision movement, can be found at http://www.slate.com/id/2148034.
I think the main difference between male circumcision and female genital mutilation is the intent behind the practice.
Although in these days of frequent bathing and high standards of hygiene it is not self-evident, the removal of the foreskin had, in different times and hotter climates, a distinct medical benefit attached to it. Dirt accumulated under the loose foreskin may cause infections and incapacitating diseases in the penis.
I am in agreement that this custom has no bearing on present day health concerns for young boys, however I think it is important to remember that female genital mutilation has nothing to do with health benefits to the woman undergoing it, and everything to do with a deliberate attempt to undermine her sexuality and ensure she has no pleasure in intercourse to safeguard her marital fidelity.
Much has been said about the damage circumcision does to the male sexual organ's sensitivity during sex, but it must be remembered that in female "circumcision", the entire centre of pleasure is removed, eliminating any possibility of pleasurable sexual intercourse. The labia are often cut off, laying the woman open for infection for the rest of her life. The urinary passage is often damaged. Many of these women will experience excruciating pain every time they have sex for the rest of their lives - the area is so rich in nerve endings that healing is seldom complete.
While I agree with viterbiSearcher's observation of the callousness with which we treat the genital modification of males in this society, I must stress that the two issues are by no means part of the same problem, nor should female genital mutilation be treated as a subset of circumcision. This is not a politicised attempt at manufacturing a gender issue - the fact is, there are no known parallels of female genital mutilation (a parallel would be something that eliminates sexual pleasure completely for the man) in any of the societies that practice the custom on either males, females or both. It is not a "gender issue", but it is an issue that touches almost exclusively on women - much like ovarian cancer, for example.