For 1 you probably need to define other runlevels otherwise it'll use the default settings from 5
Depending on your distro there are many ways that runlevels are handeled. Many distros come with an application to do it graphically, except for Gentoo which has rc-update.
I have no clue about 2, sorry. All I can suggest is do what I did. Drop artsd entierly. I have no problems with sound anymore. It's very limiting by how it works.
No clue about apt-get, but you could try looking over the tree manuall using good old ls and cd (if there is such a thing, I think protage was modelled after apt-get)
Yes you can use it to run programs. Transgaming, people who make winex, actually announced a while ago a version of winex for applications, but apparently they haven't been doing much about it. They even had a website, the link to it, is somewhere inside the Wine Weekly Newsletters (www.winehq.org
In my expirience Wine is somewhat better with applications, but not by much. Wine and winex's capabilities in both games and applications at the moment are almost the same from what I've seen.
There's a gdm.conf somewhere in /etc I beleive. I don't use a graphical logon, but I remember setitng one up for a friend. It shouldn't be hard to read it over and find where it defines the logon image. A search through the gdm documentation for 'gdm.conf' will most likely explain the settings.
I keep usr very lage (from an 80Gb HDD, home is only 3Gb and is mostly empty)
What I do is when I have programs that want to install in home, I have a directory in /usr/local/home/andrei
and in there I move the program, then make a symmlink back to /home/andrei/ for that directory.
I think you should just remove them.. no expirience with apt-get though.
Hope this helped