I read a forum thread where users were comparing the different web deployment options for Crystal Reports. One post, by Blair Wheadon of SAP, gave a good comparison of the two different CR engines.  He compares the one that supports CR Server/BO Enterprise with the CR runtime engine that supports home grown and third party web applications. He has given me permission to post it here:

Its important to understand the differences between SAP Crystal Server, and other server reporting products based on our runtime engine.

Our runtime engine is designed and licensed to add reporting to server applications. It is a lightweight, embeddable component engine without any security or scheduling built it. It is limited to processing a maximum of 3 simultaneous report requests. It is designed to run within the web server itself. Server products like those sold by Reportal and Christian Steven depend on this limited runtime engine, and add their own scheduling functionality.

SAP Crystal Server however is the same technology used by our high-end SAP BusinessObjects Business Intelligence product, with some limitations that allow us to price it very aggressively. It includes support for Xcelsius dashboarding, the new Explorer tool for casual BI users, Sharepoint and Office integration, Active Directory and LDAP security integration, scheduling, and new Enterprise-class features to reduce the cost of ownership like lifecycle management (for promoting reports between test, development, and production), auditing, and monitoring to ensure uptime.

Unlike the limited runtime engine, the SAP Crystal Server report engine uses all the server resources available, including page-level caching, and unlimited threads to effectively manage load. Plus it now includes entry-level BI functionality like dashboard support, the Explorer tool for casual BI use cases, and support for 64-bit servers.

The major limitations are: limited to a single server, no support for ERP integration (like SAP integration or Oracle integration), mobile support available only as an add-on, and it does not include Web Intelligence. None of these limitation are material to customers looking for a simple reporting server.

It does not use CPU licensing, so you can throw as many CPUs at your reporting problem as you want (as long as you’re on a single server) , and deploy to either virtual or physical servers without any licensing impact.