Add it just below
<configuration>
So, it will look as follows (e.g. add .msg):
...
<configuration>
<configSections>
<section name="ajaxControlToolkit" type="AjaxControlToolkit.AjaxControlToolkitConfigSection, AjaxControlToolkit" requirePermission="false"/>
</configSections>
<ajaxControlToolkit additionalUploadFileExtensions="msg" />
...