I wanted to install Doom 3 on my fresh install of Kubuntu 6.10

I opened the console

sudo -i (someone said this makes me rootbut it only makes root for the console session)
./doom3-linux-1.3.1.1304.x86.run

I installed it in my home directory. I'm a regular user, not root.
It created a Doom 3 folder
I wanted to copy the pk4 files from the CDs but I can't
The owner of the Doom 3 folders is root
I was trying to copy the files from the GUI

How to uninstall?

It appears you installed Doom 3 as root into your normal user home. Simply delete the folder as root.

Never heard of "sudo -i" before, the normal way to become root is not sudo but su. If you want to run a command as root without actually changing users then sudo comes in handy and the command would be "sudo PROGRAM" in this case "sudo sh doom3-linux-1.3.1.1304.x86.run"

You could also keep the folder and just copy over the pak files as root.

Yes, I installed as root because I think the installer needs to copy files to the usr folder.
I'm not really sure. I should have just asked how to install it instead of attempting it myself.

Anyway, this is a home desktop machine. I want all the folders to be under my control so that I can use the GUI (Konqurer)

How to delete the doom3 folder and all it's contents

"rm doom3" complains that doom3 is a folder. I remember from some Linux course that it's complicated to delete folders from the console.

"You could also keep the folder and just copy over the pak files as root"

I prefer to delete and install them as a regular user, if possible.

Use the command "rm -r" to delete folders. -r stands for "recursive" which means it will delete the folder and everything in it.

Thanks, that worked and I reinstalled into the home folder as a regular user, which worked as well.

FYI, the correct place would be /usr/local/games. It will run fine from /home though. To install in /usr/local/games run from terminal:
sudo mkdir -p /usr/local/games/doom3/base/
or just run the doom 3 installer using sudo:
sudo sh doom3-linux-1.3.1302.x86.run
it will make the default directories for you. Then place the 1st CD in the drive and run:
sudo cp /cdrom/Setup/Data/base/*.pk4 /usr/local/games/doom3/base/
(The *.pk4 copies all the .pk4 files in one shot!)
Repeat for CDs 2 and 3 and you're done.
To uninstall just delete /usr/local/games/doom3 , and delete ~/.doom3 and it'll be like you never installed doom. Use the "sudo rm -r" command to get rid of /usr/local/games/doom3/base/. For safety, cd into /usr/local/games/ and use "sudo rm -r doom3" from there.

I wish the instruction were on the ubuntu/kubuntu wiki
All the wiki says is

sh doom3....run

I think it did not say
sudo sh doom3....run

I did a small search but gave up.
When I install as root it was better because it puts a link on the start menu. Perhaps installing with sudo does the same.

Installing to /home/ didn't put a link in start menu so I created it myself.

Also, I think Ubuntu/kubuntu has better 3d performance than Suse.
I had to put Doom 3 on minimum settings on Suse and I was always updating drivers, hoping it would get solved.
With Kubuntu, using the old drivers, it's noticeably better and I have settings on medium, 1024 x 768

Some other problem was present as well. It can't switch back the display settings when I close Doom3 but loggin out and logging back into kubuntu fixes that.

You can always try searching the ubuntu forums for stuff like this. That's where I got it. Ubuntu forums are so big that almost any question or problem has been answered many times already.
I don't mind answering someone's thread if I know the answer, but a lot of times you can find the answer (and maybe a few more answers) with a quick search on ubuntu forums.
Also, the ubuntu forums have a subforum for gaming. Check it out if have not seen it.