Bartz (right) sports the biggest paycheck on the list of 25 overindulged big companies compiled by proxy adviser Glass-Lewis.

She took home $39 million last year, including a $10 million make-whole payment for options relinquished when she left Autodesk , her previous employer. All this as Yahoo was pushed to the brink of irrelevance by the likes of Google .

Bartz was hired at the start of 2009 to take over for co-founder Jerry Yang, and was initially lauded for her no-nonsense manner.

But Yahoo shareholders have been complaining that Bartz has done little more than cut costs, leaving the company foundering strategically. Not that it is killing her financially, obviously: She already tops Fortune’s list of the highest-paid women.

That said, Yahoo wasn’t the worst offender in terms of paying executives too much, San Francisco-based Glass-Lewis said. That distinction belongs to Micron , the Boise-based chip company that paid its chief $8 million even as the company rolled up a $1.8 billion annual loss.

Other overpayers included Aetna , the health insurer that paid CEO Ronald Williams $18 million even as the company fell short of its financial targets; Chesapeake , which gratefully gave CEO Aubrey McClendon $19 million as the energy company was losing $5.8 billion; and XL Group , the Dublin-based insurer that gave CEO Michael McGavick compensation amounting to 8% of its full-year profit.

Glass-Lewis, which advises institutional investors voting on mergers, board elections and other corporate decisions, said the latest compensation survey shows many companies have failed to adopt policies adequately linking executive compensation to performance.

“Our research shows that there remains an abundance of bad apples that continue to accept significant financial risk in order to attract and retain executives,” the firm said. “In fact, we find it somewhat baffling that so many boards and compensation committees have not adjusted compensation programs over the past year.”

The report also notes some success stories in linking pay and performance, which it dubs its 25 underpaid companies. The top 3 there: Stock market high-fliers Amazon and Apple , and Goldman Sachs , which made the list “largely a result of the compensation committee’s decision to not make equity awards for fiscal 2008.”

Glass-Lewis said Goldman’s “apparent invincibility” was hit by April’s Securities and Exchange Commission fraud suit, later settled for $550 million, and questions whether the board’s compensation committee will be able to successfully carry out a recently enacted, “entirely subjective” compensation plan.

But “given the simplicity of the program, and the com­pany’s status on this year’s underpaid list, we believe the board should be afforded additional time to demonstrate that it can create an appropriate link between pay and performance,” Glass-Lewis said.