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It seems to me that there are two basic issues being discussed as though they were interchangeable here: corporate espionage, and anti-competitive practices. Of course, most large businesses will investigate (sometimes thoroughly) their competitors, even with the goal of finding comprimising information. This is no different from the actions of police departments, political candidates, etc., and while it may be somewhat distasteful to some of us, it is (in most cases, anyway) only information-gathering.
How that information is applied is a completely different matter; in this case, one large organization investigated another with the hopes of finding 'dirt' that could be used to further the government's case against them. Once again, somewhat distasteful perhaps, but not especially immoral, and certainly not illegal.
Microsoft's actions against Netscape were aggressive, bullying, and possible only because of their monopoly position. Anyone can hire an investigator to gather intelligence on business rivals, personal enemies, etc. Very few entities (read: international monopolistic corporations, governments, etc.) have the power and influence to directly intimidate their own partners into drastic courses of action designed to cripple another powerful entity.
Of course, Microsoft has some rights. Remember, though, that even the largest, richest corporation in the world is still not a person! It does not have any rights save those granted it by popular government. Unfortunately, in this age of the DMCA, patent and copyright rediculousness, and hands-off business regulation (read: right-wing majority in Congress, money-crazed middle and upper-classes) little is done relfecting that fact.
I personally think that any corporation as large and powerful as Microsoft should be subject to the same rules of disclosure and limitations that any democratic government must follow. Their day-to-day operations have as much (or more) effect on the world economy as major policy decisions, and their workforce (legally bound to them much like citizens) is the larger than a good many sovereign nations.
Sorry, I'm all done now. Really, I feel much better now.
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