I am debugging an application which slows down the **system** very badly. The application loads a large amount of data (some 1000 files each of half an MB) from the local hard disk.The files are loaded as memory mapped files and are mapped only when needed. This means that at any given point in time the virtual memory usage does not exceed 300 MB. 

I also checked the Handle count using handle.exe from sysinternals and found that there are at the most some 8000 odd handles opened. When the data is unloaded it drops to around 400. There are no handle leaks after each load and unload operation. 

After 2-3 Load unload cycles, during one load, the system becomes very slow. I checked the virtual memory usage of the application as well as the handle counts at this point and it was well within the limits (VM about 460MB not much fragmentation also, handle counts 3200). 

I want how an application could make the system very slow to respond? What other tools can I use to debug this scenario?

Let me be more specific, when i mean system it is entire windows that is slowing down. Task manager itself takes 2 mins to come up and most often requires a hard reboot