Everything seemed fine during the upgrade I did on my main production server, except some MySQL and libc issues that are common and which were easy to fix. Another problem that arose is related to the network loopback device. The device isn't configured during boot which causes many problems with applications that rely on it (pretty much everything as you can imagine, in my case MySQL).
I think I made a mistake by keeping the local version of the configuration files or at least some of them. This brought the system in a weird state which some configuration files are old and some new. The networking part seems to be changed a lot in the Ubuntu 12.04 release with initialization being split between files. I don't know where to start. First of all which package is responsible for those scripts (is it ifupdown?)? How can I reinstall it? aptitude reinstall didn't ask to replace files with the package maintainer versions.
By the way the machine is a VPS on OpenVZ, but other people didn't have problems.