I mentioned this in another thread, but to add it hear for consistency:
I consider them canon in as much as they do not contradict the games themselves. Same with the King's Quest novels. They are officially licensed materials, and they do definitely expand the lore quite a bit, but at the same time, I'm also perfectly content in throwing the information out the window if the games (or one of the writers, such as Roberta, Jane, or Lorelei) contradict it themselves.
To be honest, as someone who has been a member of the King's Quest community since the late 90's, I think the biggest thing that put the Companions into question was the fact that The Silver Lining takes issue with several things mentioned in it (as well as several things mentioned in the games themselves). Again, I have no problem with this, as I don't consider TSL to be canon and therefore they can do whatever they want, but at the same time, I know several people do consider TSL to have some level canonicity, and as such, find that the KQ Companion materials that contradict it to be problematic.
In the end, you can take a "George Lucas" approach, where you only consider the games canon (GL has consistently pointed out he ONLY considers the six movies...well, I guess 9 now...to be canon, and all of the other books, comics, etc, despite being licensed by LucasFilm, to be fanfiction), or you can take the "official" approach (which would consider licensed materials to be canon and write off any inconsistencies as legend or misinterpretation of history), or you can consider all of it, fan games, fanfiction, licensed materials, and original games/manuals alike, and just write off all of the inconsistencies as part of existing in a fabulously wild and crazy multiverse.

Talk to you later!
JDHJANUS
Josh