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Deploying and managing 1,000 installations of Oracle Standard Edition is a huge undertaking, with considerable management and Oracle licensing costs associated with the effort. If possible, consolidating these deployments into a centralized, perhaps RACed instance (in case you need additional scalability) would probably save you upwards of 90% of the licensing and support costs alone, not to mention the associated administration! In addition, a centralized data store running Enterprise Edition offers more critical flexibility in tuning and recovery. See My Oracle Support Document 465465.1 for full details.
If you are definitely pursuing the distributed solution, the fastest deployment may simply be building a prototype with the properly patched Oracle database and cloning the disks for the systems. This will ensure standardization, and then you might only need slight listener configuration changes on location.
Oracle Enterprise Manager Grid Control can be used with the Oracle Standard Edition RDBMS. Unfortunately, the Provisioning and Patch Automation Pack, which is used to aid you in mass deployment of patches, can only be used with Oracle Enterprise Edition. I would also advise extreme caution and testing when utilizing Enterprise Manager to deploy patches, as in my experience, it has been less reliable than using the OPatch utility when applying patches to the database.
I hope this offers you some ideas and options for your effort!
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