I found it really difficult to pick the episodes in this poll. I think the season is pretty uneaven as a whole but it's not so much due to individual bad episodes but very often because good episodes with important material have some annoying flaws.
Anyway, here's my pick:
The Search, 1 and 2: This is a good example of what I was talking about. You can't really just drop these two, and they're not bad either. But the whole mind-probing angle is problematic (though I don't mind it as much as some), the Romulan on the Defiant simply gets dropped with zero explanation later on which seems strange, and the Defiant suffers defeat in its very first episode. Still, there is some interesting character material here, I think, and there's also some interesting aspects in terms of the Founders goals and their love for Odo. The introduction of the Defiant is also an important event. I wonder if these episodes would have needed a little more development time.
The House of Quark: I wasn't sure if I should include this one or not. I enjoy the episode itself but find it a little distracting right after "The Search". I really like Quark here, it's an interesting clash of cultures and the look on Gowron's face when Quark is explaining finances is priceless.
Equilibrium: I considered dropping this one. I found it really boring in the past but have come to like it a little more as of late. It's also important in terms of Dax and a necessary precursor to "Facets" which I wanted to include. I just wish this one were a little bit stronger and not quite as clichéd.
Second Skin: I think this episode works much better than its TNG counterpart (don't remember the name) with Troi since there's far more relevance in terms of the Kira character IMHO. It gives us more background on the Cardassians, pushes the notion of a collapsing Cardassian society even further and has some great moments for everyone's favorite tailor as well.
Defiant: What could have been just a casting stunt is IMHO a great episode that ties in with background established in TNG, the Maquis storyline and the political situation on Cardassia as well as foreshadowing what is to come very, very soon. There's also some great Sisko/Dukat interaction and a really devious Obsidian Order agent in the control room. I think dropping the three preceding episodes is a good thing because it makes developments outlined in "Second Skin" more relevant to what's going on here.
Past Tense, 1 and 2: Ok, the time travel is questionable as always but I think these two episodes tell a good story, and they tell it well. There's also some great material for Sisko and Bashir. I also like how quickly Jadzia adapts to the situation. Not relevant to anything else but worthwhile IMHO.
Life Support: I was very close to dropping this one but just feel I can't. There's a lot here that bothers me which is strange because none of it bothers me on paper. I like the idea of Bareil pushing himself the way he does, I like the idea of dealing with someone losing his personality in order to survive and tackling the moral implications for people such as Bashir and I like the fact that the Bajoran and Cardassian relationship is moved forward. But...well, it just doesn't really come out right. Somehow, Bareil's slow demise comes across as silly (Robo-Vedek comes to mind) as well as unnecessary, really. I think there probably isn't much you'd need to do to correct this though I'm not quite sure what you'd need to do. In hindsight, I think I'd actually have preferred them not killing Bareil and just developing him and Kira as a couple. As it is, I feel the episode is needed because Bareil's death has to be seen, I think, and because the Bajor/Cardassia development is important.
DestinyI like this episode. It's not stellar but I think it makes some interesting use of the Emissary and the Bajoran and Cardassian relationship. Dropping "Heart of Stone", I think, benefits "Life Support" as well as the episode itself. Here, you can see some of the very first results from what was achieved at high cost on the part of Bareil.
Visionary: It's almost weird that this one works, I think, since the premise is shaky, at best. However, if you accept it, it's fun to watch and even ties in with the larger scheme - and scheming, no less. I think this could have been a good follow up to "The Search". For one, this would have been a REALLY good explanation as to why the Romulan aboard the Defiant was dropped. Secondly, it would have been interesting to consider that the Romulan on the Defiant might have been part of a backup plan or an additional plan by the Romulans to remove the Dominion threat.
Distant Voices: I've always enjoyed this one for some reason. I think it's due in no small part to Siddig's great performance especially in terms of portraying the ageing process. I think it also covers some interesting aspects about the Doctor. The one thing that strikes me as questionable is that there was no indication of his genetic enhancements which I think would have popped up in this particular situation (before you respond to this: I know WHY that topic wasn't featured here

).
Improbable Cause and
The Die is Cast: Garak, Odo, Tain, a failed common plot by the Cardassian and Romulan secret services to wipe out the Founders combined with a more than ready Dominion - what more can you ask for? Lots of build is rewarded with lots of payoff as well as further setup here. Definitely the high point of the season IMHO.
Explorers: Not perfect but I really like the relationship between Ben and Jake and I think it's handled well here. What bothers me most is that just can't see anyone building a ship like this on their own and I hate the fireworks at the end.
Shakaar: I'm not too fond of Shakaar himself but I do like the fact that we get back to Bajor here. It's great to see Winn facing a situation she can't control - she's challenged and defeated. Some great material here, I think, though not as powerful as other Bajor outings.
Facets: I'm not too fond of the idea behind this episode but then I don't really 'get' the Trills as they are portrayed. I don't see, for example, why Jadzia wouldn't know about Curzon's feelings for her. After all, she has all his memories, right? I'm willing to assume some things might get buried in the subconscious (if Trills have such a thing) but if then only after a severe trauma or the likes. I don't think Curzon's shame is sufficient to expect related memories to be buried really deep. HOWEVER, I absolutely LOVE the Odo/Curzon character. Part of me really wishes they'd have left things like this. I wonder, for example, what Curzo/Odon

would have thought of the Founders, for example. I would have also loved to have seen more of the Curzon/Sisko relationship here. Still, I'm glad this character saw the light of day if only for one episode.
The Adversary: The Dominion storyline finally kicks in again. I think the settings is great - very claustrophic. And it's clear that Odo's actions here will have consequences.
Phew! That was lengthy (I should really find better ways to spend my time

). On to the episodes I'd rather drop from this season:
The Abandoned: Basically a good episode but I just can't buy into the fact that Starfeelt wouldn't have the Jem'Hadar shipped to a maximum security location immediately. It just strikes me as silly and makes Starfleet as well as Sisko look foolish, I think. I do like Odo's motives but it's not enough to warrant including the episode, I think.
Civil Defense: I actually enjoy this episode a lot (especially Dukat's face when he gets trapped too). However, it's pretty pointless and offers no character development.
Meridian: One of DS9's worst, I think. Dax falls in love with this guy and simply wants to give everything else up to live with him? Don't buy it for a second.
Fascination: I actually found this one funny in the beginning but it's just so silly and pointless that I'm convinced the season is far better off without it.
Heart of Stone: Not bad per se but really pretty pointless, I think. I don't think anything is accomplished here: Odo's love for Kira is clear without him confessing it, the Founders obviously already know this, their desire to win Odo back is clear, and none of what is said ever reaches Kira. Plus the rock that seems to be swallowing Kira looks really crappy
Prophet Motive: I actually quite like this episode - especially Quark's reactions to the new Rules. However, it's not THAT good and it's pointless in the end so I think dropping it is a good idea.
Family Business: I find the episode mildly entertaining but little more. I don't have a hard time dropping it.