Microsoft’s MSFT new version of Windows is probably still a couple quarters away from official release, but Kaufman Bros. analyst Shaw Wu is already trying to measure its negative impact on Apple AAPL .

“With the potential release of Windows 7 in either 3Q or 4Q of this year,” he writes in a report to clients issued Thursday morning, “we believe we could finally have a Windows operating system worth upgrading to.”

It may be hard for Mac users to appreciate how much this matters to IT managers.  In the Mac world, an upgrade from say, Tiger to Leopard, is relatively painless as long as your computer has the horsepower to handle the new system.

Not so in the world of Windows. As Wu writes: “From a cost-benefit analysis, it has proven time and time again that it is cheaper for consumers and enterprises to purchase new hardware with the new operating system as opposed to buying the new OS and running on old hardware.”

That’s why Vista’s tepid reception was such bad news for PC makers. Most IT departments stuck with Windows XP, skipped a generation of PC hardware, and are now managing networks of computers that are three to five years old.

“We believe Windows 7 may finally help spur an upgrade cycle,” writes Wu.

The major beneficiary of this, he says, will be Hewlett-Packard HPQ , the world’s largest player in the PC market with broad geographical coverage. (HP is not a pure play, he notes; PCs now represent only 30% of its business.)

Dell DELL is a purer play. It also benefits if Windows 7 takes off as expected, and Wu estimates that some 80% of its business is PC related.

Which brings us to the largest U.S. manufacturer of non-Windows computers.

“For Apple,” Wu writes, “we believe there is potential headline risk more than anything,” by which he means that the stock could suffer more from negative press than from any actual technological disadvantage. He notes that Intel Macs can run Windows, citing evidence that many switchers are doing just that. Moreover, he adds, Apple has an ace up its sleeve:

“We believe AAPL will respond with Mac OS X Snow Leopard, its next-generation operating system with even better usability, 64-bit processing, better Intel INTC optimization, and better utilization of GPUs (graphics processing units), keeping it a step or two ahead of Windows 7.”

Wu is sticking with “buy” recommendations for Apple and HP and a “hold” for Dell.

See also: Windows 7: Trouble on the upgrade path