If I only want to see canonical things, in what order should I watch and read Gargoyles (1994) and its associated works?
A thing is "canonical" if series creator Greg Weisman says it is.
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The episodes are on DVD and Amazon Video, but the comics are out of print. Amazon groups the episodes into "seasons" 101-105, which do not at all correspond to the above definitions, except that "season 105" is the same as season 3. The DVDs group the episodes more traditionally.
For a while, the episodes were also available for free (legally) on both YouTube and Disney's website, but they've been pulled for reasons unknown. I'm only mentioning this because you may see other people talking about it.
Anyway, enough logistics. Here's the ordering I came up with:
If you just want to read Bad Guys, you can probably skip Clan Building #3-5, but there are several minor story connections which you will miss out on if you do this. If you have both, read them in the order shown above.
Splitting up Clan Building #6-12 into smaller chunks:
Ideally, you should read these in the order shown. However, the connections between them are weak at best, so you can skip or reorder as necessary. Stories (2) and (3) are only available as a single book, so you may as well read them in that order. All three** are dependent on #1-5, and only make sense if you've read those first.
Bad Guys is all one story. Read it from beginning to end. Don't buy individual issues,*** because you'll still need the collection for #5-6.
* A few episodes are skippable, to some extent, but most are not. A full listing of which episodes you can skip (and how much you'll get away with it) is beyond the scope of this answer.
** You can almost get away with reading #1-2, and then skipping all the way to #10-12, but I can't quite recommend it because a few things won't make sense.
*** The fact that some issues are worthless was not planned; that's just how it ended up when the license expired. You might think the license expiring would be a foreseeable event, but apparently licensing is complicated, as is suddenly rushing out comics on very short notice.