What are universe and multiverse repos? Does K/Ubuntu use apt-pinning? Does this interfere or limit what packages you install to them? I may have run into a similar problem that Jhutchins had with his Gentoo and the Wacom crap the other day. I try to remove some package from Mepis that I will never use. E.g. Gtkpod for ipod support, and a whole crap load of stuff is going to be removed by apt-get. Makes it hard to gain space my removing what you don't need. Or do a apt-get update and upgrade and a whole slew of stuff stops working right.
The repo's are software that's not on the cd's, it works with ubuntu, it's been packaged for ubuntu but not "officially" in the base distro. This is why redhat is 5 cd's, and ubuntu is 1, but ubuntu has more pacakges.
apt-get update only updates your database of package, apt-get upgrade upgrades the packages. I've never had one fail. It's the upgrade process is highly tested, and is a lot different from the gentoo update process. as far as jhutchins problems the other day, they were from a developer releasing a bad package.
does apt-get remove things when you try only to remove 1 package, yes. if your package isn't a top level package and stuff depends on it. That stuff gets removed. It has to otherwise it will no longer function. The software would say "i can't find libxxx.so", and not run for you anyway. if it's a package that has nothing depending on it, say gtkpod for ipod support, then nothing will be removed. cause while gtkpod is USED by other packages, it's not required for using a music players. ( "plugin" ).