Season 1: Encounter at Farpoint--I don't like Q in the second half and Troi is unwatchable in this episode. But Q's speech about mankind is at the heart of the episode for me. It's a very interesting debate.
Season 2: The Measure of a Man (really hard not to pick Q Who?)--I think Patrick Stewart is at his finest, as is Brent Spiner in this very rich and thoughtful episode.
Season 3: Who Watches the Watchers?--I don't mind alien-of-the-week stories. I thought this one was particularly powerful and I wasn't about to waste my pick on BOBW, part I when I'm sure other people are capable of picking that one.
Season 4: First Contact--This is probably my favorite episode in the series. Season 4 is my favorite, but the wonderment of the scientist, Picard at his diplomatic best, the fear that would grip our society and the effect of space travel on our culture, it speaks to me on so many levels.
Season 5: Ensign Ro--Michele Forbes does some fantastic acting in this episode. She really gives a heartbreaking performance. It was hard just to choose one from this season as well. I wanted Darmok here.
Season 6: Chain of Command--Head and shoulders the best episodes of the season. Yes, I am including them both. Stewart and Warner shine.
Season 7: Parallels--Basically, every storyline we didn't do, was included in this episode. Themes and possibilities, from the peacefulness of the Bajorans to the effect on the Star Trek universe if we had stayed at war with the Borg past BOBW, is covered in this episode. It's so much fun to play with the universe like that.
This would've been easier to do if I wasn't limited to picking one per season, if I could just pick and choose my favorites across the seasons. However, I played by the rules.