Does Eclipse have a feature that lets you search a project to find all calls to deprecated methods?
[Updating eight years later, for current versions of Eclipse, with screenshots.]
First, build your projects. Once you've built your projects, the Problems view includes deprecations by default. You can group all the deprecations together.
To show the Problems view, use Window>Show View>Problems.
If deprecations don't appear after the next step, you can configure them in Preferences under Java>Compiler>Errors/Warnings.
Group deprecations together using the Problem view menu. Start by clicking the control circled below.
Once you've done that, open the "Deprecation" subtree. For example: