Too many to choose just one show, and each has its good eps.
WIth B5 it would be a short list of which ones weren't good. I feel the same way about Farscape, and I can't think of any Firefly eps that weren't great.
I think my favorite Stargate SG-1 ep is the "Groundhog Day" episode. "If at first you don't succeed, try, try, try, try, try, try, try again."
All the Trek series had good ones, from TOS "City on the Edge of Forever" and "Doomsday Machine" to DS9's "Paper Moon" and the one ( forgot the title ) where Sisko's dictating a log entry struggling with getting his hands dirty with Garak's help in securing Romulan support in the Donimion War.
X-Files had great ones as well, both in the main story and the one-shots.
And, of course the new BSG. The ones that weren't great for the shoot-em-ups were still great for the story, I'd say that series was the best overall since I can't think of a single episode that wasn't great in one way or another.