Here's the next batch:
25. Tinker, Tailor, Doctor, Spy (Voyager)
Aliens observe Voyager covertly using the Doctor's interface, but soon learn all is not at it seems. Robert Picardo creates a tour-de-force performance when the Doctor is caught in his Walter Mitty-type fantasies. This is one of Star Trek's funniest episodes.
23. Rightful Heir (TNG)
Spiritual doubts lead Worf to a Klingon monestary where Kahless, the originator of the Klingon religion, returns from the dead. Ron Moore takes his revision of Klingon culture to its height, fleshing out the "Klingon Jesus" and putting Worf back into a power struggle at the center of the Empire. Robert O'Reilly is once again superb as Gowron.
24. Duet (DS9)
Kira interrogates a Cardassian who may be an infamous war criminal. This is the ultimate "two people in a room" story. It's carried by a bravura performance from Nana Visitor as she's swayed first one way, then the other by her discussions with Darhe'el/Marritza, and the final twists are just as agonizing for us as they are for her.
22. Mirror, Mirror (TOS)
Kirk, McCoy, Scotty and Uhura find themselves in a parallel universe where the Federation has become an evil empire. This episode spawned seven episodes of DS9 and Enterprise set in the "Mirror Universe," and for good reason. The bearded Spock, the treacherous Chekov, and the scheming Sulu each made fantastic counterpoints to the characters we know and love.
21. Twilight (Enterprise)
When Archer loses his long-term memory, T'Pol must confront him each day with the news that their mission to stop the Xindi failed and Earth was destroyed. Enterprise takes the well-used alternate timeline idea and turns it into a touching story of unrequited love. This is Enterprise's finest moment, not because of the outstanding special effects, but because it allows its characters to be human.
20. Blink of an Eye (Voyager)
Voyager becomes trapped in orbit of a planet where years pass every second. The best of Voyager's hard sci-fi high concepts gives Kate Mulgrew and Robert Picardo a chance to shine. Lost's Daniel Dae Kim has a nice guest role.
19. Trials and Tribble-ations (DS9)
Sisko and crew are thrown back in time, and must prevent history from being changed by finding a sabotaged Tribble. DS9's characters are seamlessly merged into footage from TOS' "Trouble with Tribbles" in a brilliant homage for the series' 30th anniversary. The story has just the right balance of humor and historical reverance and adds perfectly to the original.
18. Measure of a Man (TNG)
Picard must defend Data's existence as a sentient being when a Starfleet scientist wants to disassemble and mass produce him. Trek's best courtroom drama has Picard and Riker argue opposite sides, and Whoopi Goldberg makes a great cameo in a key scene. The story achieves a nice balance, moralizing without being preachy.
17. Star Trek II: The Wrath of Khan
Khan attempts to avenge himself on Kirk with the ultimate weapon. The best of the big screen Treks boasts superb performances from Shatner, Nimoy and Ricardo Montlban. Spock's death scene is still moving more than two decades later.
16. The Trouble with Tribbles (TOS)
Kirk faces a crisis on multiple fronts when Klingons, bureaucrats, saboteurs, and Tribbles come together on one space station. Trek's best comedy puts slapstick in sci-fi, and deals with a real-world problem at the same time. Scotty's confession after starting the bar fight is still hilarious.