I finally feel like I've got a good feeling and understanding of the new CRM email router. Most of understanding came from deploying it multiple times and reading multiple documents. I don't want to go into too much depth because each deployment is a bit different and the document links below will say everything that I would say...only better. However I will say a couple of things that I've learned.
There are a few new settings for users to choose from when setting up your user profile for email.
1. Forward Mailbox - just like 3.0, you need to set up a forwarding rule through the Rule Deployment Wizard.
2. Email Router - the email router looks directly at your mailbox and sucks everything in it up into CRM. So, if you have ten's of thousands of emails, tasks and appointments in your mailbox, you may either want to not choose this option or change your setting to this on Friday at 5pm. I once set multiple people to this setting in a short period of time and CRM came to a griding halt. Make sure your server can handle this kind of intake before you do it and do it in a reasonable deployment schedule
3. Outlook Client - this is what Outlook users should user
The Planning Implementation Guide goes into those definitions a little bit more so if you want to know more about their differences check there. It's not much in that doc but there are a couple of key definitions explained there.
Here are the links that should help you out with better understanding the Email Router:
Microsoft Dynamics CRM 4.0 E-mail Router Readme (On-Premise and Microsoft Dynamics CRM 4.0 Service Provider Editions)
Microsoft Dynamics CRM 4.0: How to configure the on-premise E-mail Router in different deployment scenarios
Microsoft Dynamics CRM 4.0 Implementation Guide
Hope this helps make sense of the new functionality and setup. I know it helped me.
Dynamic Methods Inc.