Dealing with canonicity is really difficult when talking about Zelda games. Basically because the definition of canon itself, as the OP puts, depends on what fans and developers think of the games. My old portuguese teacher even liked to ay that "canon" is like a canyon: everything that is inside is canon, everything that is outside is not.
In my opinion, the original NES games are canon, obviously, even though they don't have much in-game story. Without them, there would be no Zelda series after all.
The only SNES game, LttP, is also canon, even though the newest game version (the GBA one) should be considered the most canonical one. The manual from the SNES version has more storyline though, and should be considered the most canonical one.
The Satellaview games are a difficult issue. BSLoZ has no storyline connecting it to any other Zelda game. It's about a young boy in his own world that is teleported by a fortune teller to a world created just as LoZ Hyrule, but that isn't the same place. The backstory is also different, using many elements from LttP instead of the original LoZ.So i'd say BSLoZ is not canon. BSLttP is just as BSLoZ, except that it has no original storyline. It's just a version of the LttP story, so, even if it was canon, the GBA version of LttP would have retconned it. AST is, in my honest opinion, canon. It was featured in the Zelda no Video documentary and it was referred to as a Zelda game by the devs. the staff that worked on it was also the same staff that worked on LttP, and the story is clearly a continuation of LttP's.
The N64 games are, of course, canon, with the newest version of OoT (not necesserily the Master Quest, but just the normal game with the Mirror Shield changed) being the most canonical one.
The GBA games (talking about OoX and LA) are, as well, canon. LA for being created by the same team that had created LttP and for being an obvious sequel to it (at least at first, as proven by AST) and OoX, even though being a CAPCOM game and not a Nintendo one, for having several references to other Zelda games. Also, it is listed as a Zelda game in almost every official source one can find.
The NGC TWW is, also obviously, canon.
The Four Sourds Subseries games are canon, as well, in my opinion. They were created bythe Zelda team and have several references to LttP, OoT and TWW, and even some cameos from OoX.
The DS games are also canon for obvious reasons.
The only wii game so far, TP, is also canon for obvious reasons.
The LCD games are diffiult, I'd say that ZG&W could be considered canon, as it was re-released for the G&W Gallery recently. ZGW lacks good storyline, but could be considered canon too.
The CDi games cannot by any means be considered canon, as Nintendo does not list any of them in any offical source as Zelda games.
LCT is irrelevant. It has absolutely no storyline and all you have to do is shoot enemies to gain points. It's pretty stupid to add it to a timeline theory, imho. The same is valid for TBF.
FPTRR is, on the other hand, very story-wise significant. It connects to several games and has been made thinking about the overall storyline.
The mangas are not canon because they change the stories told in the games too much. Valiant comics are, on the other hand, original stories, so one might consider them narrowly canon.
So, I'd say that the canonical spectre would look like this:
......All Mangas.....FoE....WoG.....AoZ
.............ZGW.....BSLoZ.....BSLttP...S&D
__Valiant Comics_ZG&W__AST___LCT____TBF_____TRR______________________________
[highlight]LoZ.AoL....LttP..LA..............OoT.MM...OoS.OoA..FS.TWW..FSA.TMC...TP..PH..........ST[/highlight]
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With games inside the red "canyon" being canon, the ones on the edge being pratically canon and the ones out not being canon. The games/things that are more distant from the "canyon" are "less" canon than the closer ones...