There were probably more than a few investors and money managers who sent up a cheer, and a sigh or relief, when the clock struck midnight on New Year's Eve. Finally, the stock market nightmare of 2008 was over. Or, at least 2008 was over.

"I've been through a good number of recessions and bear markets. I'll readily admit this is the worst I've ever seen it," said Todd Parrish, analyst with Robert W. Baird & Co., Milwaukee.

"Realistically, for many, many stocks, it's been a lost decade," he said. "Great companies like Intel and IBM -- their stocks are trading where they did a decade ago."

The publicly traded companies based in Wisconsin were among those paying a heavy price. It was not uncommon to see shares of some of the state's big industrial businesses lose 80 percent to 90 percent of the value they enjoyed just a year or two earlier.

Of 60 Wisconsin companies whose shares are bought and sold on Wall Street, only seven recorded stock price gains in 2008: National Presto Industries, Marten Transport, Wausau Paper Corp., Weyco Group, Bank Mutual Corp., Merge Healthcare and Marcus Corp.

All six Madison-based publicly traded companies lost value in 2008, some as much as nearly 90 percent.

"The severity of the decline has been what's surprised me," said John Nelson, small company stocks investment director for the state Investment Board. "It's been a tough year for myself and just about anybody else who's running a stock portfolio unless they've had a significant amount of cash."

Wall Street's stats for 2008 are testimony to how stunningly terrible the year was:

• The Dow lost 33.8 percent for the year and was down 38 percent from its record close of 14,165.53 in October 2007, making it the Dow's worst year since 1931, when the country was deep into the Depression.

• The Standard & Poor's 500 index, the indicator most watched by market pros, lost 38.5 percent in 2008 and is down 44.8 percent from its 2007 high of 1,565.15.

• The Nasdaq composite index fell 40.5 percent during 2008 and ended the year off 44.8 percent from its most recent high in October 2007. The tech-heavy index peaked at 5,048.62 during the dot-com bubble at the start of the decade.

MGE fares best

Of the six local stocks, MGE Energy, parent of Madison Gas & Electric, fared best, closing 2008 at $33.11 a share, down less than 6.7 percent from a year ago, at $35.47.

(The Wisconsin stock prices, and percentage change, for this year-end report were provided by Baird. The prices are adjusted for dividends and splits.)

The other local utility stock, Alliant Energy, ended the year at $29.21, off 28.2 percent from last year.

Alliant shares peaked in spring 2007 at $46, after the company sold some foreign investments, including a stake in a Brazilian utility business. The drop was probably caused, in part, by the decline in utility stocks in general, Parrish said, as well as the summer floods in Iowa that nipped earnings, and regulators' rejection of a rate increase.

Another factor: The troubled economy has hurt manufacturing, closing some plants and reducing shifts at others.

"Let's face it: The General Motors plant in Janesville uses electricity," Parrish said. That plant ended most production Dec. 23.

As for the other local stocks:

TomoTherapy and Great Wolf were engaged in proxy fights over control of their companies as their stock prices plunged.

Sonic Foundry shares rode out most of 2008 below $1 a share.

Anchor BanCorp Wisconsin stock tumbled sharply over the year.

Anchor's shares have been under pressure because the company is facing "several significant challenges," said Jason Werner, vice president of Howe Barnes Hoefer and Arnett in Chicago. Among them: "a considerable level of nonperforming loans and assets, which is likely to go higher, given economic conditions," Werner said.

Anchor also was facing a Dec. 31 deadline to reduce a line of credit by $56 million. That has been extended until March 2 under an agreement between Anchor and its lenders, effective last Tuesday.

Sonic Foundry faced delisting from the Nasdaq market, until Nasdaq suspended its rule that stocks trading below $1 had to switch to the bulletin board. Sonic stock is down 69.5 percent and closed 2008 at 43 cents a share.

Great Wolf shares ended the year at $1.54, down 84.3 percent from their close at $9.81 a year ago. The company went through a shakeup in 2008 after a group, the Concerned Great Wolf Stockholders Committee, successfully negotiated to get Eric Hovde, chief executive of Hovde Capital Advisers, and Richard Murray, also of Hovde, elected to the board of directors.

Great Wolf chief executive John Emery resigned in May and Kim Schaefer took over Jan. 1.

A key issue facing Great Wolf is the refinancing of a $76.8 million mortgage loan on its Mason, Ohio, property. "Until this is resolved, the uncertainty is likely to weigh on Great Wolf shares," wrote analysts William Crow and Paul Puryear of Raymond James & Associates, in a Nov. 5 research note.

But they noted "better than expected results" in the company's third-quarter earnings, which showed net income up 23 percent over the 2007 quarter, and added, "We remain intrigued about the longer-term prospects for Great Wolf," rating it "outperform."

After flying high with its initial public stock offering in May 2007, TomoTherapy's sales and stock price suffered in 2008 as the global economy soured and competitors mounted heavy pressure. The stock closed 2007 at $19.56 but a year later closed at $2.40 a share.

In December, the company, which makes radiation therapy machines for treating cancer patients, cut its staff by 12 percent, a move expected to save $5.4 million a year.

Even so, TomoTherapy is likely to report a net loss for 2009 with "significant challenges" facing the company this year, analyst Jeff Johnson of Robert W. Baird wrote in a Dec. 19 research note. He cited growing competitive pressure, and tight capital budgets and funding access for hospitals and clinics.

"We believe TomoTherapy's Hi-Art system will continue to stand out as the 'gold standard' in the industry from a treatment-quality standpoint," Johnson wrote. But with falling orders and global economic woes, "we believe questions regarding TomoTherapy's long-term viability remain high," he added, rating the stock "neutral."

One large shareholder, Avalon Portfolio, has nominated its own candidates to fill four of the nine seats on the board of directors and is pressing for the company to consider selling itself or entering a joint venture to restore shareholder value.

Third Wave Technologies is no longer on the list of Wisconsin stocks; the Madison company, which makes products to test for a variety of medical conditions, was purchased in 2008 by Hologic, a Boston company.

Other state stocks

Bucyrus International lost 62.7 percent of its stock value in 2008.

Shares of Joy Global peaked in June at $87 but ended 2008 at $22.93.

Both mining companies were smacked by the global recession, reducing demand for commodities, a turn that emerged in late summer, Parrish said.

Truck manufacturer Oshkosh plummeted from $47.26 at the close of 2007 to $8.94 this Dec. 31, off 81.1 percent.

Industrial machine manufacturer Rockwell Automation's stock was at $68.96 a year ago but closed 2008 at $32.25, a 53.2 percent drop.

Building and vehicle controls systems maker Johnson Controls was down 49.7 percent from a year ago; retailer Kohl's Corp. fell 21 percent, and all the bank stocks took a hit.

Harley-Davidson fell 63.8 percent. "We know what's happening here," Parrish said. "As things have worsened, it's hard to justify spending $25,000 on a bike and it's difficult to get financing to buy that $25,000 bike."

'A better 2009'

In the end, the 2008 stock market news is not all bad, said Nelson, who noted that the state Investment Board holds shares of Great Wolf, TomoTherapy and Anchor.

"For investors with a reasonable time horizon, when do they make their most money? When money is invested in a bear market. There are always going to be a number of exceptional buying opportunities," Nelson said.

At the same time, he said, interest rates are low in the U.S. and elsewhere, while some countries are increasing their money supply, and the Obama administration is talking about tax cuts. "That should help make it a better 2009," he said.

Parrish said his biggest fear is that consumers will shy away from the stock market after 2008's numbing losses. "I hope young investors don't sour on the market and never come back again," he said.

The Associated Press contributed to this report.