In the days and weeks following the sudden arrival of Mac clone maker Psystar three months ago, Apple watchers waited for the inevitable lawsuit. And waited. And waited.

Yesterday the wait finally ended when ZDNet discovered the lawsuit, filed July 3 in the U.S. District Court for Northern California. A case management conference is scheduled for Oct. 22.

The suit details numerous transgressions, including copyright violations, trademark violations and violations of the terms of the Mac OS X licensing agreement.

Florida-based Psystar began selling its low-cost imitation Macs under the name OpenMac in mid-April. It quickly changed the product’s name to Open Computer, as if that might quell Apple’s ire.

In June Psystar added the OpenServ 1100 and OpenServ 2400, clones of Apple’s Xserve, a server model Apple sells mostly to businesses.

Psystar’s famously inexpensive clones (the cheapest model was $399) did not include the OS X Leopard operating system. That was $155 extra, but the company would gladly pre-install it. Still, Psystar’s offerings significantly undercut Apple on price.

As the lawsuit makes plain, Apple had plenty of legal objections to Psystar’s operations.

So what took so long?

Maybe Apple’s lawyers wanted to take some extra time to ensure they had covered every possible argument. Maybe they wanted to allow Psystar to function long enough so the violations would pile up and appear more egregious to the court.

Apple absolutely can’t afford to lose this one; more clone makers would spring up overnight and create all sorts of headaches.

Not only would Apple lose customers to such entities (as they are to Psystar now), but having more Mac clones in the marketplace also would destroy Apple’s vertically integrated business model of “making the whole widget.”

One other possible holdup could have been Apple’s reluctance to test the End User License Agreement (EULA) in court. Many have contended for years that the highly restrictive EULAs, common to most commercial software since the early days of computing (though no one ever reads them), often contain provisions that would be struck down if legally challenged.

Many tech-savvy users have violated EULAs because they’re virtually impossible to enforce against individuals. How would anyone know?

But Psystar clearly has violated Apple’s EULA, and back in April almost dared Apple to sue: A Psystar employee who identified himself as Robert told Information Week then the company would welcome a legal challenge from Apple.

Perhaps that bluster was justified when Psystar’s plan was simply to sell computers capable of running Mac OS X. But the lawsuit alleges that Psystar tampered with the Leopard code to get it to run on its clones. Modifying someone else’s code and re-selling it unquestionably breaks the law.

Apple’s suit also alleges harm to its trademarks. “By misappropriating Apple’s proprietary software and intellectual property for its own use, Psystar’s actions harm consumers by selling to them a poor product that is advertised and promoted in a manner that falsely and unfairly implies an affiliation with Apple.”

As for damages, the lawsuit not only asks the court for a permanent injunction to stop Psystar from selling Mac clones, but also seeks a recall of all the machines it has sold. (Good luck with that.)

Given the weight of Apple’s charges and the company’s deep pockets, Psystar doesn’t look to be long for this world. Even now (mid-day Wednesday), the Psystar Web site is offline.

Several lawyers quoted in Ina Fried’s Beyond Binary blog indicated that Psystar has virtually no chance of survival.

While some cheered Psystar’s unauthorized Mac clones as rightful competition for Apple, others (me included) considered it dubious.

I remain convinced that Mac users ultimately benefit from Apple’s control of all aspects of the Mac experience. Anyone who doesn’t like the Apple Way can buy a PC running Microsoft Windows or use the open source Linux operating system.

I won’t be sorry to see Psystar go.