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Microsoft’s fight against Apple’s attempt to trademark the phrase “App Store” took on new significance last week when Apple sued Amazon.com over its use of the phrase — and tried to get the MiKandi adult “app store” to stop using it, as well.

Those developments mean Microsoft is no longer waging this battle just for itself, but effectively representing would-be “app stores” everywhere.

And in a legal filing today (PDF, 13 pages) Microsoft cites Amazon’s new “Appstore” for Google Android devices as evidence that other companies need to be able to use the phrase to accurately describe their mobile application marketplaces.

Microsoft argues that Apple’s bid for exclusive rights to “App Store” is “at odds with the growing list of competitors using ‘App Store’ in their names and ‘app store’ to describe their stores, including the Amazon Appstore, launched March 22, 2011, by Amazon.com, Inc., the world’s largest online retailer. The filing continues, “These uses, despite Apple’s continuing enforcement campaign, show beyond dispute that there is a competitive need for the term.”

Microsoft’s core argument is that “App Store” is a generic term — like “shoe store” or “toy store” — that shouldn’t belong to one company. The company reiterated its position in its legal filing today.

Apple strains to keep “App Store” for its exclusive use, even claiming that its online stores are not real stores, only metaphorical ones. But Apple cannot escape the hard truth: when people talk about competitors’ stores, they call them “app stores.” You don’t have to look far to find this generic use – The Washington Post, The New York Times, The Wall Street Journal and even Apple’s CEO Steve Jobs. And generic use of “app store” is not obscure or occasional as Apple would have us believe. It is prominent, ongoing and, by Apple’s own measure, hundreds of times more frequent than the thin generic use in the cases upon which Apple relies.

In previous filings, Apple has argued that the public associates “App Store” with its own mobile marketplace, and that many of its competitors have had no problem finding alternative terms — including Microsoft with its own Windows Phone Marketplace.

Apple has also noted the irony of the situation, given Microsoft’s past battles over one of its most famous trademarks. This was Apple in a Feb. 28 filing in the case (PDF, 63 pages).

Having itself faced a decades-long genericness challenge to its claimed WINDOWS mark, Microsoft should be well aware that the focus in evaluating genericness is on the mark as a whole and requires a fact-intensive assessment of the primary significance of the term to a substantial majority of the relevant public. Yet, Microsoft, missing the forest for the trees, does not base its motion on a comprehensive evaluation of how the relevant public understands the term APP STORE as a whole.

The issue is now in the hands of the U.S. Trademark Trial and Appeal Board. There’s no sign that Amazon or MiKandi plans to stop using the phrase in the meantime.

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