KeyRemap4MacBookの(Use PC Style Home/End or Use PC Style Home/End #2)を利用しても、
Eclipse上でHome/Endで行頭/行末移動ができなかったため、以下の設定を行った。
private.xml
<?xml version="1.0"?>
<root>
<item>
<name>For PC Users (Original)</name>
<item>
<name>Use PC Style Home/End #3</name>
<appendix>(Change Home to Command+Left)</appendix>
<appendix>(Change End to Command+Right)</appendix>
<appendix>(+ Change Home to Control+A in Emacs,Terminal,X11)</appendix>
<appendix>(+ Change End to Control+E in Emacs,Terminal,X11)</appendix>
<appendix></appendix>
<appendix>{{ PC_STYLE_BINDINGS_IGNORE_APPS_DESCRIPTION }}</appendix>
<identifier>remap.pclikehomeend_except_eclipse</identifier>
<include path="/Applications/KeyRemap4MacBook.app/Contents/Resources/include/checkbox/snippets/pcstyle_homeend_ignore_apps.xml" />
<block>
<only>EMACS, TERMINAL, X11</only>
<autogen>__KeyToKey__ FROMKEYCODE_HOME, KeyCode::A, ModifierFlag::CONTROL_L</autogen>
<autogen>__KeyToKey__ FROMKEYCODE_END, KeyCode::E, ModifierFlag::CONTROL_L</autogen>
</block>
<block>
<not>{{ PC_STYLE_BINDINGS_IGNORE_APPS }}</not>
<autogen>__KeyToKey__ FROMKEYCODE_HOME, MODIFIERFLAG_EITHER_LEFT_OR_RIGHT_COMMAND, KeyCode::CURSOR_UP, ModifierFlag::COMMAND_L</autogen>
<autogen>__KeyToKey__ FROMKEYCODE_HOME, MODIFIERFLAG_EITHER_LEFT_OR_RIGHT_CONTROL, KeyCode::CURSOR_UP, ModifierFlag::COMMAND_L</autogen>
<autogen>__KeyToKey__ FROMKEYCODE_END, MODIFIERFLAG_EITHER_LEFT_OR_RIGHT_COMMAND, KeyCode::CURSOR_DOWN, ModifierFlag::COMMAND_L</autogen>
<autogen>__KeyToKey__ FROMKEYCODE_END, MODIFIERFLAG_EITHER_LEFT_OR_RIGHT_CONTROL, KeyCode::CURSOR_DOWN, ModifierFlag::COMMAND_L</autogen>
<autogen>__KeyToKey__ FROMKEYCODE_HOME, KeyCode::CURSOR_LEFT, ModifierFlag::COMMAND_L</autogen>
<autogen>__KeyToKey__ FROMKEYCODE_END, KeyCode::CURSOR_RIGHT, ModifierFlag::COMMAND_L</autogen>
</block>
</item>
</item>
</root>
上記の設定をすれば、Eclipseでも問題なくHome/Endで行頭/行末カーソル移動が実現できた。