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I've interviewed more than 80 software consulting companies while building my own solution, PMRobot, with very similar requirements to the ones you've listed above.

The most popular web-based tools for consultant developers are currently:

  1. Basecamp
  2. Pivotal Tracker
  3. Microsoft Project
  4. (Spreadsheets)

PMRobot has the concept of 'internal' tickets that are hidden from clients, but we don't allow a way to hide a developer ticket from another developer.

In just about any tool I know of, you'd need to break the project down into multiple sub-projects to have that sort of control.

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