As with all the other AWS services you can have your limits lifted upon request.

Can the 10GB per domain limit be raised on SimpleDB? Or do I have to promise to refer to it as DynamoDB to do that? :-)

Does that apply for the 50-per-account cap on S3 buckets as well?

I'd imagine S3 falls within the scope of "all the other AWS services"...

The fact that you can make composite keys should make that irrelevant.

Edit: to clarify, I think that composite keys would make your problem limited to 256 distinct applications, not, for example, 256 customers, users, etc.