First of all: there's no need to put the SERVERPROPERTY in a subselect. You can place it in the outer SELECT.
Second: the EXCEPT is similar to the NOT IN statement when using it on a single column. If you use the NOT IN you are not bound to the "equal number of columns".
Try this:
SELECT
SERVERPROPERTY ('ServerName') as [ServerInstance],
d.name as [Database Name]
from sys.databases d
Where name not in ('Msdb', 'Master', 'model', 'tempdb', 'DBA')
and name not in (
select REPLACE(name, ' - Backup Job', '')
from msdb.dbo.sysjobs
)
order by [Database Name]