I've noticed that some questions in the canonical answer list are CW and some are not.
Is there a reason for this distinction? Should all canonical Qs be CW? If not, what is the criteria for this?
Hmm... as a general rule I think questions we create with the intention of making them canon should always be created as Community Wiki. We're creating them with the intention of throwing lots of votes on them and getting people to reference them (and probably upvote the question and answer(s) -- It seems wrong to me to gain huge amounts of rep from that.
Questions we discover and canonize I don't have strong feelings about, but I'm inclined to say they can stay in whatever state we found them (or whatever state the system puts them in as a result of any editing).
If it's a really good canonical question and has a really good canonical answer I think the users who wrote the question and answer respectively deserve the rep they'll gain. It further incentivizes writing really good questions applicable to a large segment of the System Administrator community.
I'm not sure what the rep rules are as of this moment with regard to converting a question to CW. But if the conversion either revokes existing, or otherwise stops additional rep for the questioner/answerers --
If the canonical question became canonical, spontaneously on its own accord, then no, I don't think it should be made CW.
If the canonical question was created explicitly to be the canonical question, then yes, I think it should be made CW.