Since I haven't seen a large chunk of Season 4 (and no, January can't come too soon) and I last saw Season 5 when it first aired, I'm hestiant to really decide on my favorites. But as of now, I'd have to say that overall it has to be Messages from Earth. It was one of the first episodes I ever saw, and the first that really got me interested in the series. After watching it again with the box set, I find it's the one that I rewatch over and over. There's just so much to it--G'Kar writing his book, a killer epilogue, Sheridan's dilemma, Marcus, Dr. Mary Kirkish, the unearthed Shadow vessel on Mars--plus, the direction of Michael Vejar just raises the tone of the story to a whole new level.
The runners-up are, in order:
2. Comes the Inquisitor
3. Sleeping in Light
4. The Long Twilight Struggle
5. Interludes and Examinations
Also, I have a certain fondness for A Late Delivery from Avalon and All Alone in the Night.