All the original movies and TV shows are canon, even the ones we don't individually like. Mind you, there's "ignored" and there's "contradicted." No one is in a hurry to write a sequel to "Spock's Brain" for obvious reasons, but that's not the same as treating it as 'non-canon" or whatever. We can't just contradict any given episode or series just because we feel like it.
"Canon" and "quality" are two very different concepts that don't relate to each other at all.
As for reference materials, I must say that researching old Trek episodes is much easier in these days of the internet, Memory Beta, ebay, Amazon, etc. I'm old enough to remember walking all over Manhattan one hot afternoon trying to find a VHS copy of "The Counter-Clock Incident" which I hadn't seen in years but wanted to rewatch for research purposes.
Nowadays, we have a lot more resources. Ideally, one would always want to go to primary sources (i.e. the actual movies and episodes) instead of a website or reference book, but, on a practical level, it depends on what sort of information you're looking for. If I'm writing a sequel to "The Conscience of the King," of course, I'm going to rewatch the actual episode, probably several times, but if I just need to remember what planet "Wolf in the Fold" took place on, or the name of Chekov's old girlfriend in "The Way to Eden," I'll probably just pull down a reference book from a shelf rather than taking time out to fire up the DVD player.
And if I'm brainstorming ideas for new TREK book, I'll probably consult Memory Beta just to make sure I'm not re-inventing the wheel.
