The other event that happened in 1969 that I think affected everyone was the moon landing. Like JFK's shooting, I remember exactly where I was that summer and listening to the radio as the astronauts talked. Hilton wanted hotels on the moon. Don and Roger once discussed John Glenn's parade in an earlier episode. I wouldn't expect the better part of an episode to center around it, but I'd be surprised if it wasn't mentioned.
You're right--that does seem like another one that would be important. I could easily imagine an ep ending with everyone in their own space watching it on TV, for instance. And even if they didn't feature it in an ep I'd expect some reference to it. Imagine someone saying "They can put a man on the moon, but..." for the very first time!
They have kept their eye on that aspect of the 60s, after all. You mentioned John Glenn, and of course there was also the "pictures from space" conversation between Pete and Beth Dawes and later Pete and Harry (and I think someone pointed out that after that Pete had the picture taped up in his office). It's something that gives people a different perspective. Born in a barn; died in a skyscraper etc.
I'm glad you brought up the Tate/LaBianca murders. After all the bro-ha-ha surrounding Megan's choice of T-shirt in "The Better Half", I'm wondering if the fact that she seems to be going off to pursue her acting career in California would start fueling the rumors again. It would be conceivable that she, out of all the characters, would be most likely to run into that crowd.
I thought that too. Not that Megan will literally hang out with Sharon Tate and encourage Don to get a Jay Seibring haircut, but if she's an actress in California she'd be plugged into the Hollywood scene on some level and in that scene the fringes can be the darkest place to be. (Charles Manson himself basically lived there.) There seemed like a real point made in Tale of Two Cities about how the California in Don's mind was being replaced by something else. He no longer fit in there the way he did in those early Jet Set days. Neither did Roger. But Danny did (even if he still wasn't cool) so that to me hinted at something interesting.