Does the transponder test have to be in date to sign off the annual inspection?
ANSWER: The scope and detail of an annual inspection is outlined in FAR 43 Appendix D.
The transponder test is an operational requirment of FAR 91.413 and is outside the scope of FAR 43 Appendix D.
However, even though not specifically stated in Appendix D, other requirements such as airworthiness directives, component overhaul and inspection requirements and life-limited parts should also be checked for compliance during and annual inspection. This would include the transponder operational inspection.
It is best to inform the owner/operator that this inspection is due.
You could sign off the annual inspection of the aircraft and note in the logbook that the transponder test is due and needs to be performed prior to operation in controlled airspace as outlined in FAR Part 91.