all exe. files on my HD are tainted. Please HELP

I don't know how to explain this. This is second time i've got "something" i've never seen on other computers. After playing some games from old C64, Sega and Amiga with emulators, i've got message " 16 bit sub system" or something like that, and after restarting computer, almost all my exe. files (programs) on HD are 276KB or 133KB, and when i run any of them, i got message that they aren't downloaded right or they are tainted vith viruses. After that i may not restart comp. Black screen, must go to safe mode, system restore, and i got windows again.
First time i formated almost everything, but i have no strengt for doing this again. Does anybody know what to do?
T H A N K S

all exe files means all your folders have converted to exes' or all the files in your computer have converted to exes' ??? Because there 's a virus going around these days which converts all your folder in to exes'. most of the time your folders can be recovered by choosing show hide folders and files and tick also including system files in the folder options