You can modify the main_menu.xml file (for me on Ubuntu 12.04 this was in /usr/share/mysql-workbench/data/). After you modify it, you'll need to restart MySQL Workbench.
It'll look like this
<valuetype="object"struct-name="app.MenuItem"id="com.mysql.wb.menu.query.exec"><linktype="object"key="owner"struct-name="app.MenuItem">com.mysql.wb.menu.query</link><valuetype="string"key="caption">Execute (All or Selection)</value><valuetype="string"key="name">query.execute</value><valuetype="string"key="command">builtin:query.execute</value><valuetype="string"key="itemType">action</value><valuetype="string"key="shortcut">Modifier+E</value></value>
The second to last line (Modifier+E) was edited by me. Previously it said "Modifier+Shift+Return". Note that this is NOT an alias (you cannot have both).
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
http://stackoverflow.com/questions/12043478/customizing-keyboard-shortcuts-in-mysql-workbench
You can modify the main_menu.xml file (for me on Ubuntu 12.04 this was in /usr/share/mysql-workbench/data/). After you modify it, you'll need to restart MySQL Workbench.
It'll look like this
The second to last line (Modifier+E) was edited by me. Previously it said "Modifier+Shift+Return". Note that this is NOT an alias (you cannot have both).