Each of the series had some really great shows. What I really like about the Trek series is not all the Sci Fi affects, but the stories. One that really stands out for me in the original series. No, not Harry Mudd's memorable Tribbles. Anyone familiar with the original syndicated series can attest to this.

City on the Edge of Forever
Kirk, Spock and McCoy going back in time. Kirk falls in love and knowing the woman must die, is torn in saving her at the risk of altering the future. Spock's non emotional assessment in advising Kirk adds to the dilemma. McCoy's outburst towards the end, one to see.
Of note there are a few great episodes that plays on Spock's inner discipline of his "rational" vulcan and emotional human side.
Next Generation also has some great stories, a DVD must get is the Jean-Luc Picard Collection.

Family
This one is a classic! Piccard reunites with his brother, a healing process occurs after years of rivalry between the two brothers. The wine offered before Picard leaves Earth, "Be sure not to drink this alone"; really moving. Interesting in how a followup episode shows where the wine is shared, a goodwill between nations.
The Inner Light
As in Family, another great moving story. Interesting telling of a long lost civilization by allowing one to relive an individual thru a dream. The flute!
There was also another episode unfortunately not in this collection. Picard is trapped in a wrecked shuttle and kept alive by a young cadet Wesley. The awkward dialog, the older Picard's envy of Wesley's start of an adventure in life.
Okay am I a Trekie? In a sense I guess, over all the great stories. So this brings me back to this grand character actor, William Windom who died this past week.

The Doomsday Machine
Story of Commodore Matt Decker bent on revenge of an Alien Planet Killer who killed his crew. An intriguing similarity as in the Moby Dick vengeful Captain or the Skipper in Jaws, all bent on getting the beast. The half crazed guilt portrayed in Windom is amazing, should have gotten an oscar. He reprised his role 40 years later in Star Trek Phase II.