From recollection as I just got done watching it:
Apollo's hand and the Tholian web had me in stitches.
Loved Tendi's subplot and her doing her own thing! TNG movies should have done that sort of thing.
Great take in the doppelganger trope!! (great visual of the Cerritos heading back to the rift, too - the direction is stellar)
Am definitely glad they didn't do an arc of doppelganger Marriner - I would have been interested, yes, but the subverting of expectation was expertly handled and made it even better. (Hmmm, is it possible the alt-crew might return?)
Beard. And the arc that I'm sure will follow regarding the PADD.
Loved both T'Lyns.
Rutherford's double being near-Borgified makes one wonder. The one thing I do recall, in stumbling on, is that I believe there is a Borg episode later this season. Don't tell me either way.
The "Blue Orions" (?) look like villains you'd find in the late-70s "Superfriends" cartoon. That just added TO the episode's charm.
I'm sure I missed some of the references and in-jokes. That's okay; they'll be prominent in re-viewings and the fact the story is put into consideration first and isn't relying on "a show of references" is as terrific as ever.
Can't believe this is the last season, if they're still putting out strong material.
9/10