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Is there any cloud computing service like e.g. Google’s AppEngine or Amazon’s S3 out there, that allows me to use JDBC without using some sort of proxy? I do have a MySQL server, that I can’t move into the cloud, so I want to access this server directly via a JDBC connection.
If you can’t migrate your database, don’t move to the cloud. It would be a performance and security nightmare to have your app communicate with the database over the internet.
To answer your question more specifically:
S3 is a storage platform, so it is irrelevant to your question. Google’s App Engine is only designed to interface with it’s own storage system.
If you really want to do this you could use a full fledged virtual instance such as Amazon EC2, or Rackspace Cloud.
EDIT
I forgot to mention, Google now offers a MySQL service. I would assume that Java apps use jdbc to connect to it.