I recently posted a comparison of the engine used by CR Server/ BOE and the runtime engine used by application developers. The key difference is going to be in performance, especially in high volume environments. For those of you who still plan on using the runtime engine there is a great pair of documents that explains how to get the most out of your hardware/software combination.
The first one is newer and is designed to help you select the most appropriate engine for your deployment and explain the differences between the engines. It then highlights the advantages of the more expensive engines while giving you a method to estimate the number of supported users in the runtime engine. The one thing that this document doesn’t do is provide specific techniques that you can use to maximize throughput of the runtime engine. But there is an older document that fills in this gap. I have confirmed with the folks at SAP that this older document still applies in .NET runtime deployments.
If you have any trouble locating these documents because the links have changed, please let me know.