There has been some pretty complicated issues with this server, once again. My current hypothesis is that the combination of badly configured backup processes and the buggy CUPS server together filled up the root disk, leading to a situation where MySQL database was not able to start any more. And that led e.g. me being unable to log into Ubuntu regularly via Gnome desktop. Also, it appears that either caused by this mess, or regardless of it, my main data disk (external USB Lacie) had got its “superblock” corrupted — and I did not find a way to fix it so far.
Well, luckily it was possible to log in via console, and (with some help) I have now deleted enough stuff from the root so that this system runs again. I also took the opportunity and finally did some memory upgrades: firstly, the default memory chip (512 MB in this Proliant ML110 G3) was replaced by two 1 MB chips (regular Kingston DDR2 value chips). Secondly, I got a bigger disk (not USB this time) and plugged it into the second SATA slot inside the Proliant. Seems to run ok: it is Samsung Spinpoint F1 750 GB model (more info here; a promo pic below). Now, if I only can find a way to access that corrupted Lacie USB disk somehow — it was formatted in FAT so using Windows software is an option here, too. And understanding what crashed the disk in the first place would peace my mind as well.