"To get that close collaboration between the business and engineering means selecting the right people who can be both extremely technical as well as open to working with mixed, multidisciplinary teams," Moscoso said.

Zendesk, which makes Web-based help desk and support software, holds internal "hackathons" for its application developers, which helps spur innovative thinking and gets valuable projects under way quickly.

The company holds brief "stand up" meetings for its application developers. Those last between 15 and 20 minutes and give the team a chance to discuss what's new and bring up issues that need to be addressed. But for real sit-down collaboration, there are the hackathons, where developers work on manageable projects that can be completed in 24 hours, said Zack Urlocker, Zendesk's chief operating officer.

"You don't want to necessarily do that all the time, but sometimes that's a nice way to get a bunch of small projects finished all at once and give people that sense of accomplishment," he said.