I'll go through the list of the "dubiously canon" games from the first post and give my spheal about the level of canon in each game.
Oracle of Ages/Seasons are both most definitely canon.
Four Swords is canon. People will be weird and question this, but few of them come up with and post their own timeline.
Four Swords Adventures is most definitely canon, even if Four Swords isn't.
The Minish Cap is also most definitely canon. Some people consider none of the Four Swords trilogy canon, with no justification as to why Nintendo would make The Minish Cap a normal Zelda game and not be canon. Generally, it's all the ones made and published by Nintendo that are canon.
Freshly Picked Tingle's Rosy Rupeeland is probably canon material. I haven't played it myself, and I doubt it really makes any huge difference when it comes to the timeline, but I remember reading something on the forums mentioning that it ties in at the end somehow (as to how, no details were given).
Tingle's Balloon Fight DS doesn't really follow any sort of story, and thus has no reason to be canon. If you say it is, all that proves is that, at times, Tingle likes to go fly on his balloons and do whatever is done in Balloon Fight (which I've never played or watched either version of, so I'm not entierly positive on how it works.) This game was also of exclusive obtainability to certain people in Japan for preording Thing's Rosy Rupeeland or something like that (not absolutely sure what it was).
Link's Crossbow Training, like Tingle's Balloon Fight DS, doesn't follow a story, so you can't really say this is or isn't canon. It would only prove that Link has a crossbow and occasionaly goes to fight enemies.
BS The Legend of Zelda is a remake of a canon Zelda game, so the only thing in this game they added (besides enhanced graphics) that isn't canon would be the fact that the character you control is the mascot for the whole sattelite system. It's definitely Link in the canon story.
Ancient Stone Tablets is something that I'd call canon. It was made and released by Nintendo just like all the canon Zelda games, so I don't see why not (Japan Only is a horrible reason for why not). In fact, it does prove some things about the timeline, one being the fact that Link's Awakening is, in fact, a direct sequel to A Link to the Past. The other would be (if I recall what I read correctly) the fact that Ganon is dead after Link defeats him, instead of exploding but still being alive, which makes little to no sense.
As for Zelda Game & Watch (2 Games), I'm not really sure how the story in this works. If it's the same as the original Legend of Zelda, then of course it's canon. If it's not, I think it probably falls under "poor follow-up" story-wise, leaving it as NOT canon, like most all of the Game & Watch games for their respective series.
The Valiant Comic Series, I believe, has been suggested to be canon at Zelda Wiki, simply because it follows up the the original two games and doesn't really shake many plot details, making it stand there making no difference. I don't believe they ever intended anything like the comic series to be canon, though, mostly because the comic belongs to a third party and isn't really fully Nintendo-approved. I can't see them putting it in their official timeline.
The Catoon Series is pretty much the same deal as the Comic Series, except for one detail. Like the comic, the cartoon is made and released by a third party and is unlikely to be considered canon by Nintendo. In addition, I know they do throw around details about Ganon and the Triforce, so it might be harder to place comfortably. Plus, the story flows a lot like a TV-type story, which I hate with a passion.
The CD-I Games are obviously not canon. I don't need to elaborate.
As for the Super Smash Bros. games: there would be no reason for the first two to be canon, as they have no story. Brawl, however, actually has a story involving all the characters (except for the last three you unlock - plus, Sonic doesn't do much). I expect Nintendo considers this to influence most of their series; however, this is in another world, so its existance doesn't do much to the whole Zelda timeline. It might show something about the relations between Link, Zelda, and Ganondorf and involve the Master Sword being drawn again for some time, but it has no trouble fitting after Twilight Princess without shaking much. It does show Ganondorf alive and well, but I think this only shows that people can reach that world after they die (which explains the absence of his huge scar in his belly). The Subspace Emissary is something I consider connected to all of Nintendo's worlds (by characters alone), so I'm not about the be shaken on this.
Soul Calibur 2 isn't canon in Zelda. The first post points out that "the story fits," which I'm sure it does. This game is not made or released by Nintendo, however, and Link's appearance is completely meant as a cameo (all the characters as cameos in Smash Bros. is an entirely different story).
Navi Trackers was a sort of mini game (not a mini-game) packed in Four Swords Adventures. I think that this, like Shadow Battle, is meant as something fun to do with multiple players in addition to the main story. The game that it comes in altogether is definitely canon, but the fact that Tetra appears in Navi Trackers does make it a bit uncomfortable. I doubt it has any significance and is really only meant as a cameo. Spirit Tracks has some chance of explaining something about the Four Sword, possibly making this more canon, but that's a bit too early to call. (Note: Considering The Minish Cap before the split and Four Swords + Four Swords Adventures on the Child Timeline, we don't know what happens to the Four Sword in the Adult Timeline.)
