terminal: sudo chflags, chown, or chmod has no effect

Something happened to the permissions on my machine during a backup where the owner of many of my files and apps was set to System. I can no longer use a bunch of my applications... I double click them and they don't launch. Fixing permissions did not help.

I went into terminal, but doing sudo chown -R on my applications folder didn't seem to do anything at all - the owners for many contained files stayed System. Setting the -v verbose flag didn't tell me anything. Sudo chflags -R nouchg still left a bunch of apps and subdirectories set to drwxrwxr-x, even the ones of which I am the owner. How can this be? Needless to say chmod -R doesn't do anything either. I also tried all these commands on my home directory, and they didn't seem to do anything there either.

So, basically, I type in these commands, I don't get any errors but they don't do anything. Anyone have any idea what I'm doing wrong?

Thanks,
Mike