Greg, I appreciate that it's a fine line that all Trek authors walk, and I have to admit that sometimes the excessive continuity references really annoy me. On the other hand, just the right amount actually makes me feel good.
Where is that line? It's hard to say.
What would be more realistic would be to also have memories that don't refer to old episodes, but then you'd get readers who do nothing but say "what episode did that take place in?"
So you can't really win. You can just do what makes you feel comfortable.
Well, people have made the same complaint about my LEVERAGE and 4400 novels, so I probably do overdo it sometimes. But, really, it's partly an (unfortunate?) side-effect of trying to put myself in the characters' heads.
"Gee, wouldn't this kind of remind Kirk of Janice Lester right now?"
But maybe this is an instance where psychological "realism" bumps into the practical conventions of series fiction. Realistically, a guy who was briefly trapped in his insane ex-girlfriend's body would not just shrug it off like another day at the office, but so much weird shit has happened to Kirk and the rest that you can't have them dwelling on all of it all the time! (Despite my best efforts.)
Then again, I do
like the idea of the characters having memories. One of the things I loved about BUFFY was that (unlike the TOS crew) the Scooby Gang did
remember previous episodes and talked about them when appropriate, as when Xander and Willow compared notes on what it was like to be replaced by an evil twin . . . .
That's usually what I'm going for, maybe to excess!