We've recently developed a couple of Microsites on the SharePoint platform that were within the main parent website as a subsite but are in fact separate websites needing separate usage analytics reporting. We use Google Analytics and initially thought we would just place a different script in these sites so that they get in order for them to be tracked separately. However, we soon found that Google Analytics tracks by domain name and we couldn't use a separate identifier for these subsites.
We investigated the issue further and finally found a way to track visitors to these sites separately.
Profiles and Filters
The solution we found was to create a new Profile for the associated account and then apply a filter to that profile. In the filter settings you can choose to "Include Only traffic to the subdirectories that begin with" and then enter the url for your subsite, including the backslashes. See the screenshot below:
Now we can view reports, and assign user accounts (this was very key) just to that profile and not see everything from the parent site. Result.