SELECT dbo.CLIENTREP.ref, dbo.REP2.ref
  FROM dbo.CLIENTREP 
  FULL OUTER JOIN dbo.REP2 ON (dbo.REP2.ref = dbo.CLIENTREP.ref)
    WHERE dbo.REP2.ref is null OR dbo.CLIENTREP.ref IS NULL;

How do i specify that only DISTINCT dbo.CLIENTREP.ref and dbo.REP2.ref are came back?

Just write SELECT DISTINCT ...

SELECT distinct dbo.CLIENTREP.ref, dbo.REP2.ref
FROM dbo.CLIENTREP 
FULL OUTER JOIN dbo.REP2 ON (dbo.REP2.ref = dbo.CLIENTREP.ref)
WHERE dbo.REP2.ref is null OR dbo.CLIENTREP.ref IS NULL;