I think you can just move it into the cross apply
statement:
SELECT J.CustomerID, J.JobID, J.Status, J.Deleted, J.JobNo, Customers.CompanyName AS [Company],
J.DateCreated AS [Date Created], derivedtbl_1.DueDate AS [Due Date]
FROM Jobs J LEFT OUTER JOIN
Customers
ON J.CustomerID = Customers.CustomerID CROSS APPLY
(SELECT TOP (1) DueDate, JobProductID, JobID, ProductID, DepartmentID
FROM JobProducts AS JobProducts_1
WHERE JobProducts_1.JobID = J.JobID And
Deleted = 0 and
JobProducts.Serial='123456'
ORDER BY DueDate
) AS derivedtbl_1;