If you develop only GAE and GWT, and do not use any special GAE services such as mail, blobstore, memcache, you have nothing to worry about. You are attached to GAE to the extent that you use only GAE services. However, you need to see how you access the DataStore, as the low-level APIs are going to block you to the DataStore.
I have not tried using AppScale and I assume that you asked if you can host your web application on a standalone Tomcat / Glassfish server using a regular RDBMS.
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