The main problems are as follows: 1) Data privacy. Usually this is just people worrying unnecessarily, but sometimes there are legal requirements about where customer data is stored. These may be jurisdictional or geographic requirements.

2) Integration issues. Enterprise software is all about integration. The AppEngine integration story is getting better, but you'll need to understand the SAML based single-sign-on support that is built into Google Accounts and/or implement it yourself, and you'll need to become familiar with Secure Data Connector (http://code.google.com/securedataconnector/) to integrate with private data sources.