Where does Eclipse store the info about which workspace to start up with?

In

$HOME/.eclipse/org.eclipse.platform_3.7.0_155965261/configuration/.settings

there is a file

org.eclipse.ui.ide.prefs

where it is stored.

The settings have changed since this question was posted, as newer versions of Eclipse have been released.

With Eclipse Luna, navigate to $ECLIPSE_HOME/eclipse/configuration/.settings and the file org.eclipse.ui.ide.prefs contains settings like this (Windows file configuration shown):

MAX_RECENT_WORKSPACES=5
RECENT_WORKSPACES=C\:\\src\\eclipse-workspaces\\luna\\MyApp\nC\:\\src\\eclipse-workspaces\\luna\\MyOtherApp
RECENT_WORKSPACES_PROTOCOL=3
SHOW_WORKSPACE_SELECTION_DIALOG=true
eclipse.preferences.version=1

Each entry in RECENT_WORKSPACES appears to be delimited by \n with no spaces. Whenever I manually shuffle my workspaces around (which is rare, but it happens), I've had great success hand-editing this file, saving it, and having the new paths show up just fine in the Workspace Lancher/Select a Workspace dialog.

With Eclipse Juno, I can see this information in: eclipse\configuration\.settings file.

I guess you are looking for RECENT_WORKSPACES and SHOW_WORKSPACE_SELECTION_DIALOG vars.