Having spent a number of years working primarily with MS SQL Server (and hence SQL Server Management Studio for common tasks), I am now beginning to work with MySql. To date
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
<value type="object" struct-name="app.MenuItem" id="com.mysql.wb.menu.query.exec">
<link type="object" key="owner" struct-name="app.MenuItem">com.mysql.wb.menu.query</link>
<value type="string" key="caption">Execute (All or Selection)</value>
<value type="string" key="name">query.execute</value>
<value type="string" key="command">builtin:query.execute</value>
<value type="string" key="itemType">action</value>
<value type="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).