Right, but the way I THOUGHT it worked was it was one big database type thing. So like program X could screw something up which would in turn screw up the entire thing, so nothing would work right. Whereas on a Mac, program X could screw up, but it would only screw it's .plist files and not other programs stuff. I don't know, I'm not a registry expert
Unless a program is messing around in hives and keys it shouldn't be, I don't see how this would happen. Even then, there may be security restrictions that would prevent this. Like you, I'm not an "expert" on the matter. Properly written and well-behaved 3rd party software is generally limited to its own key in HKLM\Software. Anything maliciously or stupidly written and we're right back to making generalizations and Mac analogies.
And yes, "Repair permissions" is the de-facto Mac fix that you try after the tried and true reboot.
Unless it's so freaked up that you can't even run the disk utility and have to reboot into single user mode and run fsck
Modern computers are incredibly complex devices that are prone to failure on a curve proportional to user (or developer) stupidity.