Well, I really don't know how to answer this question, because I've not watched DS9 from beginning to end since 2003, when the DVD sets came out.
These days, I tend to watch episodes of DS9 on a 'feel like it' basis. I know all the episodes so well that I don't need to see any run-up episodes or anything like that. I just pull the episode I want to see off the shelf and watch it.
One of these days I will re-watch the whole thing from beginning to end - right now I am doing that with both Farscape (I'm in the middle of season 3) and LOST (in the middle of season 2). And when I do, I won't skip anything - I'll watch it all.
But as things stand how, I tend to pull down episodes on a want-to-see-it basis...and most of the episodes I pull down tend to be around themes or characters I love.
I watch and re-watch the following types of episodes:
a) any of the more hard-core Dominion War episodes - I
n the Pale Moonlight, The Siege of AR-558 (and by extension,
It's Only a Paper Moon),
Favor the Bold/Sacrifice of Angels, The Changing Face of Evil, WYLB, etc.
b) Any of the episodes in the Garak/Tain thread -
The Wire, Improbable Cause/The Die is Cast, In Purgatory's Shadow/By Inferno's Light.
c) Any of the episodes in the Bashir-as-genetically enhanced individual thread -
Dr. Bashir, I Presume, the Jack Pack episodes, the Section 31/Sloan episodes, etc.
d) Any of the Damar-as-freedom-fighter episodes...after he turns the corner and decides to lead the resistance.
e) Weyoun-centric episodes, such as
Treachery, Faith and the Great River.
f) Martok, Martok, Martok! My favorite Klingon. Especially gravitate toward episodes that feature LESS Worf and MORE Martok!
g) there are a couple of Ferengi episodes I really like -
Little Green Men and
The Magnificent Ferengi.
h) Bareil!!!! I'll watch any episode which has Bareil in it. PERIOD.

Up to and including
Resurrection.
i) Also tend to like the Maquis episodes - particularly those dealing with the Sisko/Eddington thing.
Episodes which I actively avoid:
a) any episode which deals at all with the Kira/Odo 'ship' crap. Starting with
Heart of Stone, and
Crossfire all the way through
His Way and onward. That 'ship creeps me out and I try to avoid it if at all possible.
b) both wedding episodes. *YAWN*
c) my desire to watch any episode of DS9 is inversely proportional to the amount of time Kekio O'Brien is present on the screen. Especially if she is whining.