1.
The user configuration/user data files for various programs in Linux are stored in files or directories that start with a dot and are located in user's home directory (system-wide configuration and data is elsewhere, like /etc)

For N900, that is: /home/user

These files can be listed with "ls -a"
I'll give you the commands to make a full archive of /home/user that excludes MyDocs, which is a folder that you see when you connect the phone to a Windows computer.

cd /home
tar czvf user/MyDocs/user.tar.gz -X user/MyDocs user

This means:
Go to /home
Archive directory "user" into file user/MyDocs/user.tar.gz, verbosely, with compression and exclude the directory user/MyDocs

You will see this archive in MyDocs and can copy it to your computer. The contents can be seen with 7zip in Windows.

Later edit: I've run the command myself and I see that the -X option from the tar of busybox is a bit more primitive and doesn't do what I have intended. That is, it doesn't exclude user/MyDocs from the archive. This means it will make one big file with all your music, images and what not. And you'll have to have more than 16 GB free to be able to make a complete archive. This option should work as intended with GNU tar. I think that GNU tar is available in extras-devel.

Now, rereading my message I realise that I might have confused you even more. I'm really sorry, I think the best option for you is to make more room in rootfs:

2.
To make space on rootfs, it should be enough to disable all other repositories, except Nokia Updates. I went from 84% to 75% just by doing this and I didn't need to uninstall any application.