SAN JOSE — Finding strong evidence that Silicon Valley powerhouses such as Apple (AAPL), Google (GOOG) and Intel (INTC) had an “anti-poaching” pact not to raid rival work forces, a federal judge on Friday sent the strongest signals yet of the tough challenge those companies have defending allegations raised by tens of thousands of employees.

In a 53-page ruling, U.S. District Judge Lucy Koh in San Jose found the employees have turned up damaging evidence that top executives from those valley stalwarts, including late Apple CEO Steve Jobs, made deals to not lure away each others’ most coveted workers, particularly in the engineering ranks.

The most damaging evidence Koh cited were email exchanges among the CEOs, all previously made public but used for the first time by the judge in assessing the strength of the case against the seven companies — Apple, Adobe (ADBE), Google, Intel, Intuit (INTU), Lucasfilm and Pixar.

Koh’s findings were in a decision on whether to allow the case to proceed as a class-action on behalf of an estimated 100,000 employees, which would present a more formidable legal obstacle for the companies and raise the prospect of significant damages if they lose at trial.

The lawsuit, filed two years ago, accuses the companies of conspiring to not to hire each others’ employees between 2005 and 2009 to tamp down competition for workers and allegedly to suppress pay and other compensation. The companies have settled similar antitrust claims with the U.S. Justice Department, but this suit is on behalf of the employees.

Although Koh indicated strong evidence supports the claims for many of those employees, she said there are questions about whether the lawsuit has been framed too broadly to proceed as a class action. As a result, she invited the plaintiffs to refile the case to specifically address those questions, a common development in such litigation. The ruling suggested at least a significant portion of the case will ultimately move forward as a class-action case, and a trial date has tentatively been set for next year.

The companies have repeatedly denied orchestrating a pact to not hire employees from rival tech firms and argue it would be inappropriate to allow a class action that would group together all claims against each company. They maintain they have offered proof that regardless of any exchanges among executives, employees were paid quite well.

Apple declined to comment, while Intel spokesman Chuck Mulloy said: “We continue to dispute the allegations in the case.”

Google declined to comment on the judge’s order, other than to say it has “always actively and aggressively recruited top talent.”

But Koh’s ruling cited a host of evidence to support the anti-poaching pact allegations, particularly the email exchanges among top executives. In one email Jobs told Google CEO Eric Schmidt, “I would be very pleased if your recruiting department would stop doing this,” referring to a Google recruiter contacting an Apple engineer in 2007.

In another exchange, Schmidt told Intel CEO Paul Otellini, “If we find a recruiter called into Intel, we will terminate the recruiter. We take these relationships exceptionally seriously.”

The judge appeared troubled by the evidence.

“Indeed, the sustained personal efforts by the corporations’ own chief executives, including but not limited to Apple CEO Steve Jobs, Google CEO Eric Schmidt, Pixar President Ed Catmull, Intuit Chairman Bill Campbell and Intel CEO Paul Otellini, to monitor and enforce these agreements indicate that the agreements may have had broad effects on defendants’ employees,” Koh wrote.

The Justice Department last year brought a similar case against eBay (EBAY) based on the same anti-poaching allegations, and that case is now pending in federal court.

Howard Mintz covers legal affairs. Contact him at 408-286-0236 or follow him at Twitter.com/hmintz.