My favorite collaboration tools are those that are easy to use and readily available to everyone, because you don't know who you will be collaborating with next. Although established and stable teams may use proprietary tools, or those that are included with other enterprise software packages, that's often not an option for teams that form for specific projects and disband afterwards.
Skype is my favorite general-purpose collaboration tool. It includes IM, IP telephony, videoconferencing, and file sharing. You can build your own address book based on your contacts, and exchange calling information with anyone in the world in just a minute. If you're willing to invest a small amount in a premium subscription, you can invite still larger groups. I've had as many as 20 people on a Skype call. Computer calling is free, and you can buy inexpensive Skype credits to call phone numbers worldwide. As a tool that's established and available for anyone to use, Skype can't be beat.
Depending on the organization, others might use Microsoft Lync or even a proprietary IM client. Some might need security (usually encryption and domain login), and automatic logging (often required for financial institutions). Skype and Lync will log, but you can turn it off.
Screen sharing is an essential collaboration tool. Coders can look at one another's code, and testers can share defect results. Although Skype can do that, I prefer join.me a free tool that allows you to share your screen in seconds. With an enterprise account, you can give online presentations with multiple presenters.
Web-based collaboration tools gain popularity
Benchmarking collaboration tools
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