apt-get
just because, I'm used to it, and it's the only thing I've used, a lot. I have been using synaptic lately, apparently it is the preferred method on a debian system.
apt-get update
apt-get install <package>
apt-get remove <package> - I believe this command works, even if you didn't use apt-get to install the package. As long as the file was installed from a .deb