Hi Letty,
If you are running a website with PHP / HTML web pages and MySQL Database, then you should switch to Linux and choose a control panel like cPanel or DirectAdmin on your server. If you choose a control panel with the Linux Server, then you don't need to do anything from the console / SSH. You can manage your website(s) from the control panel and you will never need to do anything from the command line.
Windows servers slow down after some time and you need to remove system clutter and unwanted cached temporary files. You can clean your windows server using "System Mechanic" a product of
iolo technologies - The PC Tune-Up Experts and improve the performance of your server.