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The IPO market might be looking a little frosty, but the M&A market so far this year has been positive enough to warm VCs’ hearts.

The median selling price through September was nearly $71 million – four times the median amount invested prior to liquidity, according to Dow Jones VentureSource. That kind of multiple hasn’t been seen since 2000.

Because M&A is affected by the stock market, the pace is likely to fall in the fourth quarter, but the total raised is sure to exceed last year. VentureSource pegs the amount raised in the first nine months at $37.3 billion, only slightly behind the $39.42 billion for all of 2010, which was the best year since 2007. (VentureSource is owned by Dow Jones & Co., the publisher of this blog.)

So far this year, six acquisitions of U.S.-based venture-backed companies have closed at $700 million or more. The biggest was Plexxikon, which Daiichi Sankyo bought for $805 million. The company, which is developing a treatment for melanoma, raised $67 million from investors including Advanced Technology Ventures, Alta Partners, Astellas Venture Capital, Pappas Ventures and Walden International. The deal includes an additional $130 million in potential milestone payments

Second place goes to another health-care company, medical device maker Ardian, which sold to Medtronic for $800 million after raising more than $66 million. Advanced Technology Ventures was an investor in that company, too, along with Emergent Medical Partners, Morgenthaler Ventures and Split Rock Partners. Medtronic also was a backer.

Those deals closed in the first half of the year. The action lately has been more on the tech side. The third-largest deal of the year – and largest of the third quarter – was the $750 million sale of PopCap Games to Electronic Arts. The price could climb by another $550 million if certain performance goals are met. PopCap raised a single round of $22.5 million led by Meritech Capital Partners.

Paul Madera, a Meritech managing director said that during the last two years, the late-stage venture investor has seen its best run of liquidity since its start in 1999. But with stock market volatility crimping IPOs, he expects corporate acquirers to become more cautious. “There isn’t as much urgency to get things done,” Madera said.

Still, large tech companies are sitting on piles of cash and competition is fierce. The most active acquirer through September was Google, which bought nine companies, three of them in the third quarter. Dell and Zynga each have made four acquisitions, tied for second on the list.