Ok when you say Windows is crying about .COM files is it running under DOS at the startup? That is a sign of 'Ohh no I deleted the wrong files on my PC.'
Many peaple who don't know much about code are led to beleave that you open a window and just type random commands into it. But if you've ever seen C++ then you'll realize that not only does it need alot of files to function correctly but programs are split into groups like subprograms, forms, (ect). Just think of these files that aren't .EXE as body parts.