When using the SMTPAppender as such:

<appender name="EMAIL" class="ch.qos.logback.classic.net.SMTPAppender">
<smtpHost>1.1.1.1</smtpHost>
<to>blah@blah</to>
<from>blah@blah</from>
<subject>TESTING: %logger

{36} - %m</subject>

<layout class="ch.qos.logback.classic.PatternLayout">
<pattern>%d{yyyyMMddHHmm:ss} %level [%thread] %logger{36}

[%file:%line] %msg%n</pattern>
</layout>
</appender>

The resulting log prints out like so:

201208161255:43 DEBUG [main] LoggingStuff.Foo [?:?] Did it again!
201208161255:43 INFO [main] LoggingStuff.Foo [?:?] Ha info - do it
201208161255:43 WARN [main] LoggingStuff.Foo [?:?] Something is about to happen!
201208161255:43 ERROR [main] LoggingStuff.Foo [?:?] Serious stuff - is it?
java.lang.Exception: Yep
at LoggingStuff.Foo.doIt(Foo.java:56) [classes/:na]
at LoggingStuff.MyApp1.main(MyApp1.java:39) [classes/:na]

Where the %file and %line parameters are not set and show up as a '?'.