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Bug-tracking tools also fall under the category of production tools and are perhaps, after version control, the most widely-used and important tools in the development process. A good piece of bug-tracking software, properly configured, becomes invisible but critical; flawed or obtuse bug-tracking software can act like barbed wire coiled around the center of a project. Bugzilla, a popular open source bug-tracking solution, is a beginning to an answer; it is so flexible and open-ended that, when used in different ways or configured differently, it can practically become a hundred different tools on its own - for good and for ill.
What most of these tools have in common is the flexibility and adaptability of their use. Teams that retain high energy and a positive outlook on their project often share an opportunistic attitude toward their tools, making as creative a use of the methods of their production as their desired final product.
One of the most neglected areas of tools use and development is also one of the most intensely utilized. Communication tools not only speed (or slow) development, they play a role in defining company culture. The use or prohibition of open Instant Messaging services is one of the many questions a studio must answer when deciding whether to go internet-free in the office.
IM services seem to be the rule in most studios, though they have their variations; some studios use proprietary instant messenger tools on local intranets only, while others use open nets but make specific "work" IM accounts and separate them from personal IM use. In either case, IM tools are the tip of the iceberg when it comes to potential communication tools.
Many studios use a system of daily reports to monitor and organize individual development and production. For some, this is as simple as saving a daily report to a text file that is checked in to a production folder on the project server or source control. Some use email. Some even use proprietary reporting software, or functions integrated with a larger project management tool.
What I have not seen, and remain curious to the possibility of, is the use of existing communication tools in an office setting. One of the objectives of the allegedly game-like Darkstar Project is Sun's intention to create a terrifyingly comprehensive and amazing virtual office tool. With increasing numbers of teams bringing on contractors or remote full-time employees, tools like this, as well as other existing virtual production software like Adobe's Breeze, are becoming more prevalent, and more important.