Canon is material officially considered part of the primary continuity. See also Wikipedia:Canon (fiction).
El Goonish Shive Canon Edit
EGS content can be divided into five categories based on it's canonicity status.
Canon is content created and declared as canon by Dan. It mostly happens in Main Universe. It consist from most of main story (except Q&A, see below, "April fools" and guest comics), some selected NewsPaper stories and possibly some images from Sketchbook.
If a NP storyline is mentioned in the main story, or has its canonical status (sometimes indicated by an embedded image of Grace firing a cannon) acknowledged in it's opening commentary, it officially becomes canon. "Assorted" or "standalone" strips are considered to have "vague canon" status. See NewsPaper#Canonicity for details.
Question and answer sections are canonicity status on its own: they are out of continuity and therefore not considered part of canon, but the explanations in them are canonical. Note that not all of those sections are named Q&A ; Question Mark part 2 is definitely Q&A section for example.
Because they directly explain stuff to us and even read readers questions, they are breaking the fourth wall.
Other universes Edit
Canonically, there are other universes in EGS. Some are just as canon as the main one, but there are also stories that take place in their own separate universe (Blank Check for Weirdness for example) and have no connection to the main universe (yet).
Rest of NewsPaper storylines and most of sketchbook, although still created by Dan, are considered non-canon.
Fan fiction Edit
There is obviously EGS-related stuff created by other people than Dan, including some parts of this wiki (hopefully only parts labeled as such). EGS-related involvement in the Crossover Wars falls under this category.