I think that you are confused in this sense. First, if you want keep enabled only main and universe repositories, check your /etc/apt/sources.list to look something like this:

##

## ...comments...

##

deb http://extras.ubuntu.com/ubuntu raring main

deb-src http://extras.ubuntu.com/ubuntu raring main

deb http://archive.ubuntu.com/ubuntu raring main universe

deb http://security.ubuntu.com/ubuntu/ raring-security universe main

deb http://archive.ubuntu.com/ubuntu raring-updates universe main

Then, from terminal, run the following command:

sudo apt-get update

to resynchronize the package index files from their sources.

After all of these are done, if you still have doubts that a certain package is from proprietary sources, you can check with the following command:

apt-cache madison package_name

For example:

$ apt-cache madison firefox

   firefox | 23.0+build2-0ubuntu0.13.04.1 | http://security.ubuntu.com/ubuntu/ raring-security/main amd64 Packages

   firefox | 23.0+build2-0ubuntu0.13.04.1 | http://archive.ubuntu.com/ubuntu/ raring-updates/main amd64 Packages

   firefox | 20.0+build1-0ubuntu2 | http://archive.ubuntu.com/ubuntu/ raring/main amd64 Packages

$ apt-cache madison wallch

    wallch | 3.01-0ubuntu2 | http://archive.ubuntu.com/ubuntu/ raring/universe amd64 Packages