A 50-year canon can be something of an albatross. I kind of agree with JJ Abrams/Disney (GASP) when they jettisoned the Star Wars Expanded Universe. Only to re-introduce cherry picked items when needed.
Same with Star Trek. We could say, OK, unless it's been on TV or in a movie, GONE. And they can go from there.
Leaving out the albatross thing jeyl addressed... I had no trouble keeping up with the canon until they started borking it after DS9 ended. Voyager got some things wrong, as did Nemesis, as did Enterprise, and it just kinda snowballed. I like Mike Okuda, but his research methods have always annoyed me. Much can be gleaned from the original series and films, especially if you look to production notes, scripts, and other things to get inside the heads of the people making them. Everything from the timeline to starship registries is mildly broken. If they'd left off with the Prime Timeline, it'd just be as it was. But anything new is likely going to perpetuate those errors further, plus adding new mistakes or misinterpretations.
As far as the books and comics... Enh. Many of those I'd say "treat as non-canon, but draw much from them". Others I feel deserve higher status. Specifically, anything New Frontier, and the DS9 and Voyager "Relaunch" series, that pick up after the shows ended. I can't speak to how they've interwoven everything further on in the novel-verse, as 1) I'm a bit behind on my reading, and 2) I'm still quietly furious at the direction they went in and after Generations, so I treat everything after Picard goes into the Nexus as his Nexus fantasy -- including him getting out. I don't like the
Enterprise-E, I don't like the
Titan, I don't like the
Enterprise-F, and so forth.
It's a little frustrating, really. I've spent years working to unkink all the problems in the timeline, all the way back to the 1960s. I've used all the known data to anchor specific referents, extrapolated from there, and filled in gaps with appropriate placeholders. And it's been such a headache undoing the careless damage done by various individuals over the decades, up to and including Gene, himself.
--Jonah