Well there are still cylons around, of course. But I can think of three episodes off the top of my head where the cylons were dealt a major strategic blow.
But I wasn't just talking about victories against the cylons. For one, there are a multitude of episodes where a successful mission did not entail major cylon casualties. "Miniseries". "Home". "Scar". "Lay Down Your Burdens".
And its a little silly just to focus on the cylons, since there are many enemies aboard the fleet itself. Does "Colonial Day" not count as an optimistic episode? What about "You Can't Go Home Again."? "Flight of the Phoenix"?
I could certainly add more to these lists. The show certainly depicts a drastic situation and dire actions on the part of the characters. But part of the series' poignancy is that it's
not all pessimism.
edit: According to imdb, Doc Cottle has been in eleven episodes so far. Not counting his season three appearance(s?). He was introduced in the fourth episode of season one. That's eleven out of thirty (pre-season three) episodes he's been in. Roughly every third episode.