Ok, think I know what you mean. Here is some to be going on with which I beleive to be quite common sys 'problems'
What is your backup strategy?? Rsync? Bash script??
Have you got wireless network up?
How about firewall??
Or router for several boxes, maybe a samba server?
Sound up and runnig ok??
K3B, any permision issues?
Intrusion detection, have you played with LIDS?
Removable devices, CDs/DVDs, cameras??
Gpg/encryption, integration with email client?
Just some of the issues I have enjoyed learning about on my setup and I suspect many of us 'newbies' go through.