Are there good resources ( manuals, tutorials, etc ) to start studying the code of the Quake 3 engine beyond the code itself?
I'm very interested in know how it's structured for educational purposes and maybe to do some modifications.
So, you should start by looking at Wikipedia's article on id Tech 3. That can be augmented by Brian Hook's GDC talk summary and some old stuff on the Element 61 blog. In addition to that, you'll have to trawl through a bunch of whatever old mod tutorials you can find to try and reconstruct what's going on.
I'd suggest starting from the original source release from id, instead of ioquake3 or what-have-you, in order to really see the context of what's going on (how input is handled and directed inside the engine, what sort of underlying event structure is used, etc.).
Some key points that helped me when I was working with it:
Some neat things I've made for it with a coworker:
Personally, I found that the engine was a great combination of really smart things done in really dumb ways, really dumb things done in really smart ways, and really smart things done in really smart ways. It's a great example of how to have modularity and good structured design in a medium-scale C project.
Lastly, don't feel bad if it takes a while to grok. It took me maybe a month to really be able to know where to find what I was looking for in the engine; if all else fails, start at the application init and just tunnel down into the functions, leaving comments for yourself as signposts. My monitor ended up covered in pink post-it notes with function names, line numbers, and short descriptions of what they did.
The book Focus On Mod Programming in Quake III Arena will help you understand the way the client and server logic are decoupled, client prediction, client side graphics effects etc.
http://en.wikipedia.org/wiki/Quake_engine is a good overview of what is out there, but you can get into the details of its architecture quite quickly through its citations.
May i also suggest a couple books on game engine architecture which may be more in line with what you are looking for. While not Quake specific, they go into the details of engine design and run parallel to many aspects of of the Quake engines: