I looked at this post and it seemed to be close to what I want, but my case might be a little worse:
Basically a while back I (very stupidly) changed the permissions on all sorts of system folders, and eventually rendered my computer virtually unusable. I managed to hack administrator privileges back onto key folders and getting it working, but in doing so I only modified permissions a lot more away from the natural state. I'm looking at this icacls stuff, but ultimately I need to reset EVERYTHING back to what it was in The Beginning, before I messed with it, from the C: directory all the way down. Right now application data is what's giving me problems, and I can't get it to work no matter how much I fiddle with those specific permissions.
I will be forever grateful for help on how to do this without having to reformat.
Update: I've found that it's in an odd position where I may have set the permissions for something more or less correctly, but any and all automated actions (like running batch operations from an elevated command line or trying to apply changes to subfolders) will still tell me "access denied." However if I manually navigate to those folders and simply try to open them, Windows tells me that access is denied, but that by clicking "ok" I can permanently give myself access to it, and that fixes problems. This is great except in order to fix this I have to manually open every folder affected, and there doesn't seem to be any pattern to it. How can I fix this!?