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To exclude annoying packages or classes when doing automatic organisation of imports with Ctrl+Shift+O create a a “Type Filter” under Windows → Preferences → Java → Appearance → Type Filters
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Most annoying for me are JUnit 3, awt, Joda time:
java.awt.* junit.* org.joda.*
Source: http://blog.vogella.com/2009/04/01/eclipse-organize-imports-filter