It depends on what type of information and whether it is for the Unix layer or the GUI layer. You will find you http.conf, .bashrc, and so forth are just like on unix. From there you will find thing in Library/Preferences at both the user and system level. Oh yeah don't forget the goodies off in netinfo.
I'm not looking for something in particular, I'm just curious to understand the start-up process, with its global part and its user specific part. Also to understand where are the shared variables (like name of the favorite browser, ...)
All the common preferences for basically all of the Apple stuff is at /Library/Preference in the plist files.
Individual user preferences are stored in your home directory at ~/username/Library/Preferences or /Users/username/Library/Preferences, which are the same directory.
A lot of the UNIX stuff is in /etc which you can't see in the Finder unless you type in the path directly into the Open Folder command.
Like lurk was saying, OS X uses the NetInfo database on startup for a lot of the configuration such as where to find the user's home directory.
Netinfo is sort of like the Windows registry but doesn't seem to slow down the computer when there are a lot of things added to it. One reason is because you don't use the Netinfo database to store all your preferences for applications like a lot of programs do in Windows.
Netinfo stores a lot of information like static hosts, instead of using a hosts file to add static host entries.
Well the startup process runs in basically three phases. The initial startup is very unix like and is driven by the rc and rc.* stripts in /etc this handles the very early startup and also the case of booting into single user mode. On the whole though not very much is done with the RC scripts and nothing should really interact with them. The majority of things that would have been done in rc.* under Unix is handled by a program called SystemStarter that liven in /sbin.
SystemStarter is responsible for executing the various "Startup Items" most of which live in /System/Library/StartupItems but can also be found in /Library/StartupItems. This is where the meat of the process is taken care of look at the man page for SystemStarter and search for startup items and you can find out more specific details.
I was able to write a startup item to customize the firewall on my G4 in a hour or so if googleing. It is easier once you have the right terminology.
None of this is user specific and it all runes before the login window appears. CaptainCode already touched on that aspect of the process above.