After months of spending my time writing down my ideas, finally I've got the time to put into a readable format, as an encyclopedia. However, there are a lot of threads I did not close yet, and in general, I'm unsure of the directions of expansions.
In general, if I put my worldbuilding project into such a format, what are the things I always have to keep my eyes on? Are there such things at all, or is this question too broad?
What you're talking about is developing a system for organizing information. A visual chart would probably be quite useful.
Within your universe define a list of major events which constitute its very foundation. Those are the ones that you should make sure are fleshed out, and that you would document first. For example:
A creator type being comes into existence.
Then, the progression becomes natural. For each major event, create a list of important minor events which stem from it.
It creates minions/companions, which become minor Gods, or angels. A point of contention arises between them, and some turn away from the Creator, and become "creatures of darkness".
Now you're really cooking. Make a "tree" of events which stem from one another, and just start documenting each branch. It will become visually apparent when a set of linked events are missing a connected piece, which you will have to explain before those original events start to make sense.
Good luck!
As stated, your target is to organize information. And that is usually not a trivial task : information elements are linked to others, may be linked to space and/or time. So you can have different axis : you can for example use a geographical map to locate things in space, a timeline to organize them in time, some family tree coupling time and relationships between siblings, etc.
Depending of the level you want to achieve, it can be quite a lot of information to keep in your head. You may want to use some tools to organize this. It can be simple notebooks and papers, or some software (I can think of the great Tiddlywiki here ; feel free to add suggestion in comments).
If you are building this for a world or game, do not push it too much, as the world is mostly a recipient for your story, and not an end by itself. Structure your information around the hero or center of the story.
As a side note, you can maybe find inspiration for both content and organization in some gaming systems like Microscope.
