Been a few years but we finally upgraded our web servers to the latest and greatest DELL Poweredge servers. It was a major pain making sure that hundreds of websites and databases all were moved and setup correctly. Just a few tips from our experience. If you have hundreds of websites setup in IIS, you will most likely have advanced configuration for some of them like URL Scan, IIS filters, etc. So it is best you just migrate to the same OS configuration as long as you are running windows server 2003 or greater (yes we are a Microsoft shop ). We host our servers at RackSpace and highly recommend them. You pay a lot but the service is top notch.
So for our web server they recommended we use a software package called DoubleTake. It really made the process much easier. It basically is software that will mirror the entire operating system, keep track of file system changes, and finally move the configuration to the new server. The catch is the OS and server process must be of the same type. The backup of our system took over a day to complete so make sure you do this over the weekend when traffic is low. Also make sure your servers are on the same network if possible or have a very high bandwidth pipe between them using a VPN. Overall it went without a problem and there was only a minor configuration with IIS. If your servers will be assigned new IP addresses you will have to re-bind your websites with those new internal IPs. There are fast ways to do that but that is another post.
Finally our DB server was the biggest upgrade since it requires the most processing power. We have hundreds of databases and most used mssql 2000 so it was worth the upgrade. We chose to upgrade to windows server 2008 64-bit version. We also upgraded to Microsoft mssql 2008 64-bit version. This version removes the limit of roughly 3gb memory usage on the 32-bit version to terabytes. So we were able to upgrade from 4gb memory to 16gb of usable memory. This makes a huge difference. It is recommended to either know what you are doing or hire a DBA for this. The best way to do the migration is to move the .mdf and .ldf files to the new server, use scripts to attach the databases, then finally use some more scripts to move the logins and passwords. This is the quickest way to move hundreds of databases reliably.
Our email server is managed by rackspace's own proprietary email software so that is not an issue for us.
Hope this helps save some time for you!