[Nate the Great]

ODO: It sounds like there was a power struggle on board, some sort of attempted takeover.
O'BRIEN: Management by mutiny. Standard operating procedure on a Klingon vessel.

Not really. I don't think that "mutinies" in the traditional sense really happen on Klingon ships. They're not needed. All it takes is one guy to challenge the captain to a fight to the death (making sure the challenger gives one of the acceptable reasons for said challenge, of course). He wins, and the crew decides whether his reasons were valid. If not, another duel, and so on.

KIRA: And O'Brien. Either we get a more reasonable commander from Starfleet, someone we can control, or we go it alone.

Oh boy is there a lot to unpack here, but I think I've already covered most of it.

ODO: Computer, open a channel to Starfleet Headquarters.

I find it doubtful that anyone in the Militia would have access to Starfleet Headquarters. No wonder that admiral was mad at Kira before. Why would they answer a call from Odo? If anything I would think that Odo would have a direct line to someone at Starfleet Security and someone else at Starfleet Intelligence, and THEY could inform Starfleet Command if necessary.

O'BRIEN: An hour ago. I've heard some disturbing rumours from our people on the Promenade. I think she's going to make an attempt on your life.
SISKO: I want you to arrest them. Kira and every Bajoran officer on this station.

Since when does O'Brien have control over the Starfleet Security forces? Has Primmin already been reassigned, this is his job, isn't it?

The Fiver

Kira: You are going to support me in my battle against the Federation, a.k.a. El Diablo, aren't you, Odo?
Odo: Um... of course... what is it that you want me to do?
Kira: Send the fleet to the forest moon of Bajor. There it will wait... until called for.

I assume that this is an Endor reference. It seems like a bit of a stretch, but okay...

Odo: Hm, perhaps the log entries from the Klingon ship will reveal something to me about this strange phenomenon...
Klingon Captain's Log: Dear Diary. Today my Operations Officer killed my Tactical Officer. Then the Chief Engineer killed my Operations Officer. Then the First Officer killed the Chief Engineer. Finally, I killed the First Officer.
Odo: Damn, nothing unusual there...

Is anyone else reminded of the Old Lady that Swallowed a Fly?

O'Brien: Commander, we're outnumbered. We have to go away and find reinforcements!
Sisko: Are you crazy? As soon as we leave, she'll attack us with this fully armed and operational battle station!

Yeah, definitely Return of the Jedi. The station won't be "fully armed" until "The Way of the Warrior". As for "fully operational", I wonder if O'Brien ever felt confident making that declaration.

Odo: Doctor, I finally got it! The spheres from the Klingon ship are making everyone go evil!
Bashir: How did you come to that brilliant conclusion, Constable?
Odo: Shhh...
(...)
Spheres: Evil, evil, evil...
Bashir: Oh, I see.

Which does beg the question, what were these things trying to accomplish? Does fomenting conflict enable these things to reproduce? Were they a Dominion plot to conquer without weapons?

Sisko: Good. It's been over a week now. Did you allow the Valerians to dock?
Kira: No.
(Sisko throws his clock at Kira at Ludicrous Speed)

Yeah, whatever happened with the Valerians, anyway? Was Sisko or Kira right about that?

Memory Alpha

* "The reason writer Joe Menosky had Sisko making a clock was to try to convey to the audience that he had become "an obsessive quirky Emperor Rudolph-type" who fussed about with mechanical bits and pieces." Yeah, this reference was way too obscure. I've never heard of the guy, which means obscurity in my book. At least if you do the research, the reference makes sense. Rudolf neglected his duties to engage in his hobbies, which included art and the occult. I don't see any particular reference to clocks in his Wikipedia page, instead it seems like a celestial globe (i.e. a map of the stars visible in the sky) would be more applicable.
* The Saltah'na clock appeared in a number of other episodes. I particularly remember him fiddling with it when talking to Worf in "Hippocratic Oath."

Nitpicker's Guide

* The Klingon ship somehow continues to transmit a transporter signal after it's been destroyed.
* Phil jokes about turning on the close captioning for the Klingon transmission, since everything the Klingon said was in the captions.