Can you use DB2 Connect in your environment ?
DB2 LUW has a powerful set operator, EXCEPT ..
(
select 1,2 from sysibm.sysdummy1
union
select 3,4 from sysibm.sysdummy1
)
except
select 1,2 from sysibm.sysdummy1
will give you the result as (3,4)
You can create federated connections to the tables and then issue the queries from your workstation ... Of course, this may underperfrom for large tables
HTH
Sathyaram