of suggestions..and questions...
Could you post some of your system specs if possible? Ram, make of PC, etc...?
When did this begin?
Did you download or install anything new recently that may have caused this?
Do you have something like "Windows Defender" blocking things from running? Look in your task bar or the arrow expander in the task bar, show hidden icons, see if security center flag is there, check Defender to see if it's blocking items.
Also, if you don't know or it worked fine recently, a restoring from a good known restore point may work.
You have done scans it seems with some security tools and found nothing, did you try and boot into safe mode and see if anything will run?
It almost sounds like someone ran msconfig and set it to selective startup, or you have some security blocking your apps.
Help! I have Windows 7. I can't open any program except for Internet Explorer (64-bit). I can open a limited number of things on control panel. I've run both the AVG and Kaspersky Rescue discs with nothing found on both. I am unable to download any new anti-malware/virus programs. My AVG is turned off and I can't get it to turn on. Also programs like Adobe flash player is turned off/disabled. What can I do? I'm decent with a PC but not real tech savy so please give me some info in lay terms if possible. Thank you very much!