The top executives of the taxpayer-backed companies stand to make millions of dollars in salary, deferred pay and long-term incentive awards for 2010 – including substantial sums that are performance-based, at least in name.

Fannie (FNMA) CEO Michael Williams and Freddie (FMCC) chief Charles Haldeman each stand to make some $6 million this year, going by company filings that broadly outline 2009 pay and 2010 guidelines.

Using the same data and assuming no one got a pay cut — we can’t risk having the talent leave, after all — their top lieutenants could make between $2 million and $3 million each.

This for a year in which the companies saw their shares delisted from the New York Stock Exchange, posted $28 billion in losses through three quarters and ran their tab at Treasury to a startling $150 billion. Your taxpayer dollars at work.

Of course, it’s not quite fair to judge the companies by their sagging financials. Since their government takeover two years ago Fannie and Freddie have been dedicated to keeping mortgages available, in the name of propping up house prices.

“Today, Fannie Mae’s focus is on preventing foreclosures, making mortgages and rental housing as affordable as possible, and supporting the housing recovery,” the company says on its Web site.

But the vital signs in the housing market – after being briefly revived by an injection of tax-credit steroids – have been dropping too. Foreclosures are off the charts and prices in many markets are sagging. House prices now seem headed for the dreaded double-dip, which stands to deepen an already unbearable foreclosure crisis.

This isn’t to blame Fannie and Freddie for the latest housing downturn, which is being driven by much larger forces such as near-10% joblessness and overstretched consumer balance sheets.

And to be fair, the companies don’t even fully control their pay guidelines. They are set by the government via the companies’ regulator, the Federal Housing Finance Administration.

We won’t know for sure what the Fannie and Freddie execs get till February, when the companies are due to file their annual reports. However large Fannie and Freddie’s executive pay numbers might seem, surely they will be dwarfed by many of the paychecks cashed by Wall Streeters.

Still, the prospect of million-dollar payouts at these companies shows how empty the pay-for-performance talk at big companies can end up being.

In addition to their base salaries, Fannie’s officers are eligible this year for deferred pay (check issuance is delayed by a year) equal to about three times the base pay and long-term incentive awards that amount to more than double base pay.

Part of those payouts is contingent on hitting corporate goals tied to company performance and that of the housing market. That is, admittedly, a step up from the 2009 practice of paying for what Fannie delicately calls “service” – that is, the act of showing up in the morning.

Even so, Fannie’s 2010 goals are so squishy that it is hard to imagine anyone’s pay is in serious danger of being docked.

Fannie says its goals are to:

• “achieve our mission of providing liquidity, stability and affordability to the U.S. housing and mortgage markets”;
• “build a more streamlined, higher-performing company”; and
• “build a stronger service and delivery model to support the housing finance market.”

Talk about setting the bar low.

There is no doubt Fannie has provided liquidity to the housing and mortgage markets. It is so obvious that Fannie, Freddie and the Federal Housing Administration are the only things standing between us and the utter collapse of the housing markets that even the House Republicans are no longer calling for the companies’ prompt liquidation.

Similarly, building a higher-performing Fannie or Freddie shouldn’t be hard, given that the companies have managed to blow through $226 billion in capital over the past three years. And who even knows what it means to build a stronger “service and delivery model,” so it’s hard to see anyone being held to account on that one.

Fannie and Freddie referred questions to the FHFA, which declined to comment.

The easy comparisons aren’t a huge surprise, given the companies’ brush with death two years ago and the spluttering Washington debate about just what to do with them and the dysfunctional U.S. mortgage subsidy.

“For companies in transition, it’s not entirely unusual to see less fundamentally driven goals,” said Andrew Mandel, a compensation expert at Buck Consultants in New York. “Once they get their act together, you’ll usually see more financial drivers for these compensation decisions.”

And indeed, next year Fannie will replace this year’s nebulous goals with numerical ones. The top three call for the company to “reduce fixed general and administrative expenses; reduce credit-related expenses; achieve risk-adjusted return on economic capital targets.”

Freddie’s 2010 goals include some financial targets, mixed in with objectives tied to supporting administration housing programs, implementing appropriate accounting standards and operating its technology infrastructure “in an efficient fashion.”

It’s tempting to wish the companies, now shorn of the profit motive that informed some of their misguided decisions during the bubble era, would be free too of seven-digit executive payouts.

But that change will come only with action from Congress, which sooner or later is going to have to decide what it wants to do with these companies. Many happy New Years waiting for that one.