Sorry to say, in some odd way I think they're canon.
Easter eggs are not canon. If they are dr.who, godzilla, star trek are as well.
Easter eggs aren't necessarily non-truths, is what I'm saying. There's a difference between a simple nod to a certain phenomenon and an expansion built around it. To me, when you buy something that was created by the developers, it's canon, ESPECIALLY if it is a DLC pertaining to a specific product. Fallout 2 is irrevelant. This is Fallout 3 DLC, as in 'stuff that belongs to Fallout 3', as in 'things we thought you might wanna play in addition to the game'. Whatever's gonna happen in Fallout 4 or any other next instalment is completely irrelevant, seeing as how the games are unrelated. But Fallout 3 DLC parts ARE related to Fallout 3, hence they cannot be dismissed as 'non-canon' and so they become canon.
Aliens as eater eggs only is part of fallout yes. Mothership Zeta or anything like it No.
I see what you're getting at. But then again, if MZ changes the story of Fallout to a point where it's ruined, that's really not my problem. I didn't create it. They did. Their story, their aliens. I play this stuff and forget about it pretty quickly (until next I start the game of course).
If your Fallout 3 character never enters the spaceship, then IN YOUR PLAYTHROUGH, MZ isn't canon. Then again, suppose I've never met, say, Wolfgang or anyone else in the Wasteland... does that mean they don't exist in the Fallout 3 universe?
I guess my definition of canon is pretty big. I see the Fallout 3 universe as something enormous and ridiculous and fun and beautiful and sad and crazy and weird. Everything I can possibly encounter in the game when I shove in that disc and/or download official expansion sets is canon. Because it's there, and it cannot be denied.
I get the concept of easter eggs. Mothership Zeta isn't that.
Of course, I am in no way trying to prove myself right or anyone else wrong. I love discussing these things, and coming from some really immature community boards, I have to save I love the maturity of the people here and the topics.