I think The Search
(especially part II) ranks as DS9's biggest letdown in my book. The basic concept of the Founders being Odo's people is brilliant, but the revelation happens too fast and is handled poorly overall (despite some good scenes with Odo and Kira on the Founders' homeworld). There are worse episodes, of course, by a lot, but few (if any) blown opportunities of this magnitude.
It's really the classic case of TNG-style thinking still throttling the show a bit after so much ground had been gained in season 2. As I recall, the identity of the Founders was going to be revealed later, but Piller (I think) pushed the writers to go with it right away. And then you have the TNG-esque virtual reality "twist" at the end, which was already way overused and stale at this point.
The big problem in this specific case is that the VR twist makes it feel like these episodes have a reset button at the end, when actually a major revelation has occurred that will shape the rest of the show for 5 seasons. But the way the story is told tends to undermine the enormity of the whole discovery.
Anyway, Improbable Cause/The Die is Cast
really washes away that bad taste, and the show starts moving forward again. Still, season 3 tends to rank only above season one in my mind, as far as how much I enjoy it overall. Granted, it is much better than season one.