The column t00.[CustNo] is never NULL, so you'll always end up with a value of 0.

You don't need the nested CASE, you can just add more conditions as needed.

Select t00.[InvDate]

,t00.[CustNo]

,t00.[Salesman]

,t00.[Quantity]

,t00.[ExtendedPrice]

,t00.[ExtendedCost]

,t00.[ItemNo]

,t00.[InvoiceNo]

,t00.[LineNo]

,t00.[Warehouse]

,t00.[chargecust]

,t01.[customerid] AS CustomerIdT01

,t02.[salesman] AS SalesmanT02

,t03.itemid AS ItemIdT03

,t03.[commissionperc]AS ItemComPercT03

,t04.[productfamilyid] AS ProductFamilyIdT04

,T05.[ProductFamilyID] AS ProductFamilyIdT05

,t05.[commissionperc]as ProdFamilyComPercT05

,T06.[Customerid] AS CustomerIdT06

,t06.[commissionperc] AS CommissionPercT06

,Case when [t00].[CustNo]is not null then 0

when [t02].[salesman]is not null then 0

when [t06].[customerid] is not null then [t06].[commissionperc]

when [t03].[ItemID] is Not Null then [t03].[commissionperc]

Else [t05].[commissionperc] end AS BaseCommPerc

FROM [US02301_DWH].[dbo].[Fact_InvoiceAnalysis]t00

left join [dbo].[manualNOcommissioncustomer]as t01 on t00.[chargecust]=t01.[customerid]

left join [dbo].[manualNOcommissionsalesgroup] as t02 on t00.[salesman]=t02.[salesman]

left join [dbo].[manualcommissionitem] as t03 on t00.[itemno]=t03.[itemid]

left join [dbo].[itemmaster] as t04 on t00.[itemno] = t04.[itemid]

left join [dbo].[ManualCommisionProductFamily]as t05 on [t04].[productfamilyid] = [t05].[productfamilyid]

LEFT JOIN [dbo].[ManualFixedCommissionCustomer] as T06 on [t00].[custno]=[t06].[customerid]

where YEAR([invdate])='2015' and T00.salesman='16'

order by t00.Salesman desc