Matt Yglesias notes a Ross Douthat column that invokes one of William McKinley’s splendid little wars, this one in the Philippines. He points out that the military and naval counterinsurgency effort in the Philippines worked, but then wonders if anything beneficial actually came out of it:
It seems to me that unless you look at victory and conquest as being their own reward, it’s hard to see any. Anti-American rebels lost, but we didn’t really win anything of note. We spent a lot of money, suffered some casualties, killed a lot of people and in exchange got some military bases that were overrun by the Japanese as soon as it looked like they might be strategically useful.
Knowing something of the conflict, I would go further than Yglesias: taking the Philippines was possibly the worst single foreign policy decision in American history, rivaling the one which took us to war with Britain in 1812.
First, some background. The Philippines in 1898 was one of the last major possessions of the long-failing Spanish empire. As part of its war with them, the United States destroyed Spanish authority in the islands and then purchased the archipelago in the peace settlement for $20 million. Filipino insurgents, led by their leader Emilio Aguinaldo, resented this and fought back, first conventionally and then using the tactics of insurgency. What resulted was a three-year conflict, bloody and ugly on all sides, that resulted in an American victory (the Moro Insurgency, which broke out shortly thereafter, was a distinct conflict, though putting the two together is not terminally objectionable).
The U.S. saw the Philippines largely as a stepping-stone to China. This was the era of John Hay’s “Open Door” policy, when all the imperial powers were struggling to broaden their influence in China, at the expense of each other and the Chinese. The Philippines, in addition to being seen as a new frontier for Americans, was also to be the first great acquisition for an American Empire.
The problem was that the Philippines was simply not really usable militarily. It was way out at the end of an extended supply line from the United States, 5300 miles to Hawaii and 7300 miles to San Diego. It consisted of 7107 islands, large and small, which made it essentially impossible to defend. Most critically, it sat directly on the supply route between Japan, a newly powerful military nation, and its sources of raw materials in southeast Asia. As long as the United States held the Philippines and the deep water port of Manila, where a fleet could be stationed, the Japanese felt insecure. By 1915, American strategists were already writing that:
The taking of the Philippines may be ranked among the worst military blunders committed by any American government–it is difficult to put the matter more strongly. It is a weak, ex-centric military position, fundamentally indefensible against any strong transpacific power, but inevitably a magnet to draw troops and ships away from our shores. 
Taking the Philippines essentially put the United States and Japan on a collision course out of which it was hard to steer. This was not inevitable. At the turn of the century, Japan’s attention was towards the mainland of Asia and southeast Asia, and away from the broad Pacific that separated it from the United States. It was worried about Russia, China, and the European powers that held so much of mainland Asia. The Americans and Japanese got along rather well. During the Boxer Rebellion, when American and Japanese units served together, there was quite a friendly relationship between the two. American ships coaled at Nagasaki, where they played baseball games for Japanese crowds. There was an American naval hospital there for several decades. The relationship that was building was one similar to the United States and Great Britain, two growing naval powers separated by a large ocean that nonetheless had essentially decided NOT to be rivals.
The Philippines changed that. It made America an Asian power and an Asian power that presented a direct threat to the Japanese. Coupled with the radical militarization of Japan that occurred in the 1920s and 30s, it led directly to the outbreak of the war in the Pacific, a war in which the Philippines fell almost immediately to a Japanese invasion and a war in which 354,000 American casualties (106,000 dead, 248,000 wounded; figures approximate). By itself, the Pacific War was America’s third worst in terms of casualties; by itself, about 15% of all American combat deaths in our history happened in the Pacific from 1941-1945. The Americans came again to Nagasaki, but this time with fire and sword.
Taking the Philippines put us on the line for that train-wreck. It did not particularly help us gain entry to China, despite our ongoing fascination with that nation through the early 20th century. Other than that, the conquest brought little in the way of benefits. “I shall return,” was MacArthur’s famous declaration upon leaving the islands in 1942, to which an ironic response might well have been, “Why did we come in the first place?”
Update: I highly esteem Spencer Ackerman, but he’s just wrong here:
But the hinge point in U.S.-Philippine history — what yielded the friendship and closeness that the two nations presently enjoy — was the Japanese occupation of the Philippines. What the Japanese inflicted upon the Philippines and its people was by orders of magnitude far worse than anything the U.S. ever dared. You probably know the rest: MacArthur declares he Shall Return; he does; the battle of Leyte Gulf is one of the largest in the history of naval warfare; we drive the Japanese from the Philippines; the amount of gratitude is overwhelming; a partnership has been our inheritance ever since.
American-Filipino relationships were friendly well before the start of World War II. The Japanese occupation certainly cemented them, but the reconciliation had started much earlier.
 Silbey, War of Frontier and Empire, 213.