Sorry, I've had some long work days which are limiting my time online. Let me see if I can answer some of your questions.
Nepomuk is a way of indexing files and folders to make desktop search quicker. There's really nothing you need to do, it works in the background.
As far as the "Open with" - you have to get used to the application names that certain files open with. Usually the choices given are the correct applications and you can choose any of them. Text files will give you the choice of apps like kwrite or kate, both will open text files. They'll also open program files, as they were developed to be able to deal with program languages such as Python and C++ or Ruby etc. HTML files will give you a choice of using Firefox or Chrome or Konqueror or Opera etc. MP3 or other sound files will give you the option of opening them in Amarok, or mplayer, or VLC. All will open and play sound files, and, mplayer and VLC will also open and play video files.
In KDE, I have "Disk Utility" or "Disk Usage Statistics" or "Kinfocenter" or Kwikdisk" that show disk usage. I also have gkrellm installed that shows RAM, CPU usage, Temperature, Voltage, Time online, Memory used. I find this very useful and keep it up on the screen at all times. There is no defrag in Linux, no need. Fragmentation is so low with Linux file systems that we don't worry about it.
BTW - In KDE "Dolphin", or in Gnome "Nautilus" (File Managers) can be configured to show you the file size or folder size and room left in your partitions. If you go into Settings in either app, you'll find the configure entry. Play around with the configuration. Once you apply the change, it will show up, so, if you don't like what you see, you can set it back immediately. If you go into "View" in either of their menu's, you can set the information that appears on or under the icons to display info that you might want to appear each time you open the file manager.
Root is your system administrator. It is a user just like you are on your machine. One of the reasons Linux is so secure is that the system files are owned by root, the system administrator, and, unless you log in with root privileges, you cannot access and change system files. Windows also has a system administrator, unfortunately, it is not as secure as the Linux based root. I'm just touching the surface here, but I guess it's a start.
If you want us to explain more, just ask, I'm sure others who are just starting can use the info also. Heh, just be patient, we have outside jobs like everyone else, so, we are not always here to respond right away, but, we do like to share our knowledge.
Keep us posted on how you're doing.