SELECT [PATHWAY_ID], [PAS_ID], [Patient_Name], [Pathway_Specialty], [Clinician],
       [Referral_priority], [RTT_START_DTTM], [Days Waiting], [Activity Type],
       [Last Activity Type], [Next_Appt_DTTM], [First_Appointment_Flag],
       CASE WHEN [Days Waiting] <=97 AND [Next_Appt_DTTM] IS NOT NULL THEN 'Booked'
            WHEN [Days Waiting] >=98 AND [Next_Appt_DTTM] IS NULL THEN 'Unbooked'
       END AS 'Booked Status'
FROM [GWH_RTT].[rtt].[GWH_RTT_Nonadmitted_PTL]
WHERE [Referral_priority] = 'Routine'
ORDER BY 'Booked Status' DESC

with q as (<your query here without the order by>)
select q.*
from q
where [Booked Status] is not null
order by [Booked Status];

SELECT t.*
FROM (SELECT [PATHWAY_ID], [PAS_ID], [Patient_Name], [Pathway_Specialty], [Clinician],
       [Referral_priority], [RTT_START_DTTM], [Days Waiting], [Activity Type],
       [Last Activity Type], [Next_Appt_DTTM], [First_Appointment_Flag],
       CASE WHEN [Days Waiting] <=97 AND [Next_Appt_DTTM] IS NOT NULL THEN 'Booked'
            WHEN [Days Waiting] >=98 AND [Next_Appt_DTTM] IS NULL THEN 'Unbooked'
       END AS 'Booked Status'
FROM [GWH_RTT].[rtt].[GWH_RTT_Nonadmitted_PTL]
WHERE [Referral_priority] = 'Routine'
) t
WHERE t.[Booked Status] IS NOT NULL
ORDER BY [Booked Status] DESC