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Create a default workspace with settings that are common to any new workspace.  This will make it easy to set up custom workspaces later.

First, make sure Java 5 is installed as the default JRE.

1. Go to Window -> Preferences -> Java -> Installed JREs
2. Add -> Standard VM, with Directory /usr/lib/jvm/java-1.5.0-sun
3. Select it to make it the default JRE, then click OK.
   

Your own Perspectives and Views are a matter of preference, of course.  Here's what I like to use.

1. Window -> Open Perspective -> Java
2. Window -> Customize Perspective
3. Under Shortcuts Tab, Submenu "New", also select the following:
   • Java -> JUnit -> JUnit Test Suite
   • Mercurial -> Clone Repository Using Mercurial
   • SVN
4. Under Shortcuts Tab, Submenu "Show View", also select the following:
   • Atlassian Plugin
   • Checkstyle
   • Java -> Call Hierarchy
   • Java -> JUnit
   • Mylyn -> Task Repositories
   • Other -> Merge
   • SVN
   • Team
5. Under Command Tab, also select the following command groups:
   • SVN
   • Team
6. Open Window -> Show View each of the following Views:
   • Console
   • Navigator
   • JUnit
   • SVN Properties
7. Close the following Views:
   • Hierarchy (west panel)
   • Package Explorer (west panel)
   • Outline (east panel)
   • Task List (east panel)
8. Under Window -> Preferences:
   1. General

Other Stuff

• openssh-server
• msttcorefonts
• openoffice.org
• mercurial
• hgsvn
• truecrypt
• vim-full
  ...then modify /etc/vim/vimrc to your taste.