Not really. It's just bad design.
Your server isn't getting games installed on it, which put all kinds of settings in the registry, then removed later when the game is old and tired, leaving behind cruft (including DRM bullsit) in the registry.
When a program is UNinstalled, all traces of it should be gone. Apple took a different approach, which arguably works far better. Even if stuff is left behind, it just takes up a bit of disk space, and doesn't affect the system at all.
Having leftover files and registry entries from apps that have been removed does not slow down Windows. Like any other OS, they just sit there doing nothing.
What does slow down Windows is disk fragmentation and lack of RAM.
Windows tends to have a lot of patches. Over time, these patches spread OS files across the hard disk. This leads to file fragmentation. When you are running a 5400 RPM drive, have a lot of apps installed and removed, and a lot of OS updates load files from the hard-disk slows down as the disk head has to travel a lot. Background disk defragging was first enabled by default in Windows 7. Of course, the ultimate solution for disk fragmentation is to use SSD drives as there is little penalty for fragmentation due to the high random memory access speeds.
Most Windows boxes today have at least 4GB of RAM but older Windows systems ran on 2GB of RAM. Even so, as you install more apps that have background components, they take up memory. When Windows needs more memory than what is available, it will cache unused parts of the OS and idle apps. This was accomplished by storing the cache data in the Windows page file on hard disk. When an idle app is clicked on, the cached data has to be reloaded and the previously active app needs to be cached back to disk. This whole process is really slow.
There are two ways to solve low memory issues:
1. Install additional memory: Windows Vista/7/8 32-bit recognizes a maximum of 4Gb of RAM. To install and use more than 4GB, you need to install the 64bit version of Windows. Most systems sold in the last 5 years run Windows 32-bit with 4GB of RAM or less. Only recently have systems been sold with Windows 64bit and 8GB of RAM. In my opinion, 8GB should be the minimum.
2. SSD: It might, at first, seem weird that I'm mentioning SSD in the memory section. The OS caches memory when it runs out of physical memory. SSD drives are really fast, much faster than physical drives. So, even with a system with low memory you would see a big difference using a SSD for your OS drive.
The point is that a combination of Windows improvements (background defrag on hard drives, 64-bit OS), technical improvements (SSD), and cost improvements (8GB RAM vs 4GB RAM) have contributed to eliminate the gradual performance degradation that we've seen in the past. It could be argued that adding better components to the system is just masking the limitations or design issues of the OS. But, as long as it works do we really care....
In my opinion, a Windows 7 64bit, or higher, system with 8GB of RAM and a SSD OS drive will not experience any performance issues over time for the average user. Windows performance degradation is a thing of the past....