It's hard to pick just one!
Here are some of my favorites:
"German East Africa"/"Congo" - Pure Frank Darabont brilliance.
"London" - Excellent story dealing with love and loss. I think the episode did a great job evoking wha it must have been like for men to leave their families for war.
"Vienna"/"Florence" - What can I say? I'm a sucker for love stories.
Even though they weren't originally paired together, they are one of the few re-edits that work well IMO.
"Curse of the Jackal" - I love how this episode sets up Indy at three different ages, and ties it all together with a treasure hunt story. By the end of the episode, we're definately left wanting more.
"Benares" - I've always been into philosophy and world religions, so this episode was a very enlightening experience.