The lawsuit, which accuses Microsoft of manoeuvring to extend its crushing grip on the software industry to the newly discovered terrain of the Internet, was dismissed in indignant tone by Mr Gates as "a step backwards for America, for consumers and for the PC industry, which is leading our nation's economy into the 21st century". If Microsoft is guilty of anything, it is of innovating for the good of all of us.
To fend off the devils of a bad conscience, tycoons have always armed themselves with rationalisations of their tactics. Today, thanks to the scholarship of the business biographer Ron Chernow, we have the chance to view the psychology of Mr Gates against an especially illuminating historical backdrop - the story of that other icon of American enterprise who fell foul of Washington, John D Rockefeller Sr.
With fortuitous timing, for readers and author, Mr Chernow has just given us Titan, an opus appreciation of Rockefeller that is being greeted as the most insightful and compelling read ever written about the man who created Standard Oil. He was helped especially by the discovery of 1,700 pages of notes of interviews conducted with Rockefeller himself for an authorised biography that never saw the light.
Has Mr Gates read it? He should. While comparisons between himself and Rockefeller should be taken only so far, the echoes from the days of Standard Oil - from its founding by Rockefeller in 1880 to its break-up by order of the US Supreme Court in 1911 - to the predicament of Microsoft today are, at the very least, uncanny.
It was, for example, largely as a result of Rockefeller's ruthless reign that the Sherman Antitrust Act was signed into law in 1890. It is on that same act, still the Magna Carta of US government supervision of free competition, that the Justice Department bases its action against Microsoft today.
And the two men are tied in this fashion: both stumbled at young ages upon a new element that was to revolutionise society. For Rockefeller it was oil, that first gushed from the Pennsylvania sod in 1859, and for Gates it was the birth of the computer. Moreover, each managed to gain a near-90 per cent of the market in their chosen commodities, kerosene for the one and PC operating systems for the other.
What Rockefeller committed to win that dominance, however, was surely more wicked than anything Gates could now be charged with. He crushed almost all his refining rivals by a combination of predatory pricing, industrial espionage, the secret ownership of companies that pretended to be rivals and, above all, the securing of hidden rebates from railroad companies for every barrel they shipped, not just of his oil but of oil produced by his competitors also.
One small illustration offered by Chernow: grocery stores offering kerosene from independent refiners were liable to find that, suddenly, a competing store would open across the street in which everything, not just kerosene, would be suspiciously cheap.
Most infamously, in 1872, shortly after Rockefeller did his rail deal, he perpetrated the "Cleveland Massacre", in one stroke taking over 22 of his 26 rivals in the city. The result of the Rockefeller strategy of buy out or crush was the trust - or, more accurately, the monopoly - that Standard Oil quickly became. Or the "Octopus", as contemporary reporters took to calling it.
At the heart of Chernow's book is the description of a man, who, not unlike Gates, believed that, whatever others cared to say, his achievements were ultimately all for the greater good of society. Indeed, it was many years before public distrust of Rockefeller gained politically viable momentum.
And for good reason. Rockefeller seemed to embody the qualities, beloved by Americans, of buccaneering enterprise and personal advancement. Moreover, Standard Oil cut the average price of refined oil from 23 cents a gallon to 7 cents.
Similar dynamics have applied to Mr Gates. While Mr Gates has earned enemies in his own industry, as Rockefeller did in his, for many ordinary Americans he remains a hero rather than a villain.
Most astonishing, however, is the logic that Rockefeller espoused in justifying the cruelty of his methods. Read Chernow and you wonder if the man we have considered the greatest capitalist of them all was actually a disciple of Karl Marx.
He concluded in his own mind that the free market, so keenly espoused by the new liberal thinkers of the time, was instead a pestilence that had almost crippled Standard Oil, when, in its earliest days, it had faced the intrusions of johnny-come-lately refiners rushing for their share of the oil boom. He fulminated against the "chaotic conditions in which virtuous academic Know-Nothings about business ... were doing what they construed to be God's service in eating each other up".
God, thought Rockefeller, a devout baptist, would surely have blessed his model of doing business. He genteelly called it one of "co-operation" between players on the same field; we, today, might prefer terms like cartel or monopoly. "What a blessing it was," he opined, "that the idea of co-operation, with railroads, with telegraph lines, with steel companies, with oil companies came in and prevailed."
Critics who charged him with destroying competition, had misunderstood his saintly mission. He referred once to Standard Oil as "the Moses who delivered them [the refiners] from their folly which had wrought such havoc in their fortunes". He went on: "It was not a process of destruction and waste; it was a process of upbuilding and conservation of all the interests ... in our efforts most heroic, well meant - and I would say, reverently, Godlike - to pull this broken-down industry out of the Slough of Despond."
Was Rockefeller perhaps a little crackers? How, in one personality, could two such disparate instincts be combined: the God-fearing figurehead, who, as Chernow amply illustrates, was a fine and devoted husband and father, and the ruthless conniver who knew no greater drive than the appetite for money?
"I believe it is my duty to make money," Rockefeller said, "and still more money". In the same breath: "And to use the money I make for the good of my fellow man according to the dictates of my conscience." And, indeed, the largesse of Rockefeller, also detailed in "Titan", rightly established him as one of the greatest philanthropists America has ever produced.
The singular legacy of Rockefeller, however, was surely the Standard Oil ruling of 1911. It resolved the competition-vs-"co-operation" argument by setting in stone the equation of a free market governed at the same time by strict rules of fair play. And it established the right of the federal government to act to make sure those rules are obeyed.
What words might John D impart to Gates if he were alive today? He would advise first against underestimating the power of the Sherman Act. And he would also note this irony: the dismantling of Standard Oil made him far richer than he had ever been before.