Hmm, tough call actually, since all three episodes are good, but all have their flaws.
Voyager was imaginative and cool and I loved the Voth and their city ship. Downside: the regulars felt like bit players here.
B5 has the most memorable scenes for me, especially Delenn going all scary and wrathful and the Sheridan-Ivanova scenes were some of their best. Downside: it felt a bit all over the place.
DS9 has a nice coherent story (so good they remade it twice!) that sets up how Worf and Martok's relationship will be from now on. Downside: like all these Bird of Prey episodes, it's not quite as exciting as you'd expect.
Lines of Communication
is the one that sticks in my mind the most, but I'm going to give the prize to Distant Origin
for being such an imaginative sci-fi story.