More than 96 percent of Microsoft's revenue is generated through partners, said Mark Barry, managing director of Microsoft's U.S. venture capital and emerging business team. Partners can engage a number of programs, such as Empower for ISVs, which is for early-stage ISVs to accelerate development, and the Emerging Business Team, which works with new companies. The Microsoft ISV Royalty Licensing program allows ISVs to embed some Microsoft software in their own products.

Microsoft tends to work with venture capital-backed companies because that way, Microsoft knows there has to have been a level of due diligence undertaken in order for a company to get funding, Barry said.

One ISV in attendance, however, described difficulties in fitting in with Microsoft's partnership efforts. It was difficult to get traction with Microsoft, said Patrick Gilbert, president and CEO of 4SmartPhone, which makes mobile solutions.

"We didn't have an agenda of being bought out or what have you," Gilbert said. The first company to call 4SmartPhone was not Microsoft but Palm, he said.

Jadallah responded that it was important for ISVs to know who their advocate is going to be at Microsoft.