Is there a program to see a line of commands that are being given to my pc while using it? Something like a command window that just gives a readout of all the inputs? This isn't for any specific reason other than curiosity about what's going on inside the beast.
What kind of input are we talking about? Input given through USB and other peripherals? Network input? Reads from the harddrive? And at what level? A computer receives a crazy amount of input from all over, all the time, so without knowing about all software on the web, I can almost guarantee there's no single application for monitoring ALL input.
For now I would be interested in peripheral inputs and how the OS sees them in real time. I have used wireshark for network monitoring.
Unfortunately, I don't have any particular experience with USB sniffing/monitoring, but a quick google search showed a few hits. Is it something like this you're after? http://www.eltima.com/products/usb-port-monitor/ That one isn't free, but offers a 14 day trial. I'm sure there are free alternatives out there, too (such as this: http://freeusbanalyzer.com/)