From my experience, these are the areas I wish the devs new more about:
IIS. Especially important for ASP.Net apps. A few key areas to look into:
IP Binding and Host Headers. When you create a new IIS site, making sure you know how to configure the IP and host headers correctly.
Application Pool Settings. There are a number of settings here that impact your application, including timeout values and recycling. Be sure to understand how those might impact your sessions.
Enabling Methods. If you are doing a REST API, know how to enable additional methods like PUT.
SSL Certificates. Understand how to install an SSL certificate and how the process of getting a certificate works.
Performance Tweaks. Ensure you know how to enable GZIP, disable e-tags, configure content expiration, and set cache headers. Use Fiddler to see how IIS is responding to requests. You can dramatically improve your application's performance with a few simple changes.
WCAT. Related to IIS, but understand how to set up WCAT and set up load testing for your application. That way you can have hard data on your application's response time and limitations.
Permissions. Understand what permissions need to be on what folders in your application. For example, if your app writes to a folder, do you need to give NETWORK_SERVICE access to that folder?
Windows Firewall. Seems basic, but especially for Windows Server 2008, understand how to add an entry to the firewall, set the port, set the scope, etc.
SMTP Server. Understand how to set up, configure, and troubleshoot the Windows SMTP Server. You may also want to look at HMailServer as an alternative to use with your apps. Also, read up on SPAM filtering and how to correctly create emails (proper from, to, multipart messages, etc).
SQL Server IP and Port Binding. Not directly related to Windows Server, but comes up a lot. Understand how to set up SQL Server to bind to a specific IP and port. Know the difference between dynamic and static ports, how to set up and connect to non-standard ports, how to construct connection strings using instance names and custom ports.
Many of the items on the above list are in the domain of Server Admins, but you can make yourself much more valuable if you can understand and troubleshoot those areas.