I just noticed that when I upgraded to v15.3 from v15.2, one of my calls to LABKEY.Message.sendMessage() had a significant change in output and seems to be broken. Here is some code that produces the output in question:

<script type="text/javascript">

function getEmailAddress() {
        // Need a real user's email address due to labkey restrictions on email sending
    LABKEY.Query.selectRows({
            schemaName: 'core',
            queryName: 'users',
            columns: ['email'],
            maxRows: 1,
            success: emailURL,
            failure: function() {alert('No emails found!');}
        });
}

function emailURL(data, response) {
    var email = data.rows[0].Email;
    var url='http://www.labkey.org/';
    var msgConfig = {
             msgFrom: email,
             msgSubject: 'Test of URL in HTML email',
             msgRecipients: [
                 LABKEY.Message.createRecipient(LABKEY.Message.recipientType.to, email)
             ],
             msgContent: [
                 LABKEY.Message.createMsgContent(LABKEY.Message.msgType.html,
            'A test <a href="' + url + '">link</a> to labkey.org')
             ],
             failure: function(errorInfo, responseObj) {
                alert('Failed to send email. '+errorInfo.exception);
             }
        };
    LABKEY.Message.sendMessage(msgConfig);
}


Ext4.onReady(function() {
    getEmailAddress();
});

</script>

With v15.3 I get an email containing:
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: 7bit

A test &lt;a href=&quot;<a href="http://www.labkey.org/&quot;&gt;link&lt;/a&gt;">http://www.labkey.org/&quot;&gt;link&lt;/a&gt;</a> to labkey.org

I haven't run this exact code under v15.2 (as I don't have v15.2 handy anymore), but I have some old emails created by similar code on v15.2 and I believe the output from v15.2 would be:
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

A test <a href="http://www.labkey.org/">link</a> to labkey.org

The message generated by v15.3 results in the follow DOM (using Chrome v47.0 and viewing the message in Gmail):
A test &lt;a href="<a href="http://www.labkey.org/%22%3Elink%3C/a%3E" target="_blank">http://www.labkey.org/"&gt;<wbr>link&lt;/a&gt;</a> to <a href="http://labkey.org" target="_blank">labkey.org</a>

Which doesn't seem to be what I asked for in my call to LABKEY.Message.sendMessage. Let me know if that all makes sense.

thanks,
-Will