In versions of Microsoft CRM prior to version 4 if you wanted to track emails and email replies you had to make use of a tracking token (ie. CRM:xxxxxx) in the subject of your emails.

This was required so that the email router could determine what the email was regarding. The option still exists and is still the default choice in CRM 4 but it is optional as there is an alternate method.

Microsoft CRM 4 makes use of a "smart matching technology" that has a similar effect by comparing subject lines and party lists.

The tracking token can be turned off so that this "smart matching" can be used by the a CRM System Administrator via the System Settings dialog.

For more information visit the following links

What's New in Microsoft Dynamics CRM 4.0 E-mail Integration

Microsoft Dynamics CRM, Email correlation and smart matching