Presently, I can't save files from Mail anywhere within my Home folder. I also can't save a preference file from another app. When I try to install a Mozilla plug-in, I get an error. However when I check file permissions from Terminal and Finder, I see that I am the owner of all directories with read/write permissions, and all files seem to have the same. I was able to download and install some applications in the Applications folder, by dragging them to the folder.
You might want to repair permissions and see what happens then...some strange things can happen with some system file permissions being messed up.