I’d start with the last episode of season 2 “The Jem’hadar” where you finally meet members of The Dominion.
I remembered an episode I didn’t like. “If Wishes Were Horses,” where O’Brien doesn’t battle a Cardassian, Romulan, Klingon, or Breen, he fights… Rumplestiltskin.
I agree with you so far as that goes, but would submit that Kira blows both of them entirely out of the proverbial water - she’s the great unsung Star Trek Babe of the series.
Quark always had nice looking women working for him too, like Leeta.
I also love It’s Only a Paper Moon a story featuring Nog and Vic. I think it speaks well of the series that two peripheral characters could hold an entire episode but they pull it off. One thing DS9 had in abundance was a large cast of good side characters. I know allot of fans don’t like Vic Fontaine but I do and I think he is used very well and Nog comes across as a real person suffering psychological problems.
I never really liked Ezri Dax. I always thought they this great opportunity where they could put Dax into another male host after the audience & every character save Sisko have gotten to her as female and blew it by just putting her into a younger female.
But if they had done that the show would have been Star Trek: Deep Space Sausage Fest.
They did it to keep a semi-familiar character (she’s still Dax) and to introduce some tension, primarily with Worf (dead ex-wife still haunting him in the form of another person who remembers being with him) and the other players who knew Dax.
Just too bad (but probably for the best) that they didn’t put Dax into a flamingly gay male. Now THERE would have been some ‘dramatic tension’ with Worf! 
Call to arms is definitely one bad ass episode and probably my favourite - it has two particularly outstanding shots:
5.15 - the minefield cloaking followed by Dukat and Weyoun’s reaction to it.
9.00 - watching the Defiant fly away from the station cloaking at the same time as Martok’s bird of prey, each of them making their own different cloaking noises.
And of course the priceless 0.30 - Kira being all official n’stuff. 
The only downside to it was the fact that after waiting for so long to see the station being attacked by the Dominion (finally!) we got a fight that was largely off camera and made up of recycled shots due to the fact that it was the end of that season (I’m such a geek I can even tell you where those recycled shots were from too 
).
DS9 was definitely my favourite trek, and easily one of my favourite shows too. I loved the Dominion mainly because they were played so well and grew from simply a name we kept hearing, to an unknown quantity after first met in Jem Hadar, to a distinct threat then onto a HUGE threat that at one point looked like it was going to take down the Federation. The arc that encompassed this was played brilliantly, particularly with the various parts of the Dominion acting together to make them so frightening (the Founders - can be anyone and anywhere, the Jem Hadar - an unstoppable killing machine, the Vorta - the bureaucrats from hell and utterly loyal to the Founders). This made them, for me, far more real and tangible as a complex society and threat than simply another generic race of warriors who were all uniformly bad.
I have to say that some of the Ferengi eps were okay, but on the whole they weren’t the strongest. I think my favourite one was Civil Defence where Jake and Sisko accidentally trigger an old program that was never removed from the system designed to stop a Bajoran uprising happening, and quickly find the station turn against them as they’re identified as rebels. I’d say hilarity ensues but it’s more a case of just how much worse can this situation get?
Worst - Vic Fontaine. I never actually found out how Odo declared his undying love to Kira because it involved watching a Fontaine episode to do so and I couldn’t bring myself to do it.
Fans seem either to hate Vic or love him, I’m the former.
Neither did I – my friends and I always referred to her as “Ally McTrill”, since she reminded us so much of Callista Flockhart’s then-well-known character.
I finished Season 6 over the weekend. I liked Tears of the Prophets, but was strange in a few places. Kira was on the Defiant while Dax stayed on the station? The doctor of the Defiant was on the station while the Defiant was going into battle? Kira took over for Sisko, even though Worf was next in line while on the Defiant?