The only really big difference between installing things from the Software Center or another gui and doing it from the command line is when things go wrong.
In most guis,installation error messages are hidden and they just give you a general message that it didn't work. When you do it from the command line, you see all the messages that are generated. Often, this information can be used to fix the problem or it will tell you why you probably don't want to fix it. E.g. installing the package would break or uninstall other packages that are already installed.
Sometimes, a package fails to install just because one of its dependencies is not installed (and the regular install doesn't automatically fix that like most do). When this happens, you can often just install the missing package first and then your install will succeed.
Also, apt-get will inform you of other associated packages that are "recommended" along with your package, so you can look them up and see if you want any of them.
It also reports on any packages that were installed previously that are probably not needed any more and tells you how to remove them.
You shouldn't add/delete packages from either of these last two steps without carefully reviewing the packages involved, but it's usually safe.
In Ubuntu 12.04, newly installed apps get added to the launcher by default, but this only happens for apps installed using the Software Center.