Didn't anybody like "A Rough Whimper of Insanity"? A terrific episode about the relatively early, yet increasing pervasiveness of computers and the internet, including how they tied into Tom's situation. The kid's house was very atmospheric and his ultimate fate sobering. A great show for pizza, especially since Tom was delivering pizzas!

My favorites listed in episodic order
Absolute Zero / Turnabout - An outstanding pilot and Turnabout was a good follow up. The continuity of Tom joking about assuming Bellamy's identity and then actually doing so in the next episode was awesome.
Something About Her - One of the Organization's best forms of manipulation. Also Carrie-Anne Moss is GORGEOUS!
The Spider Webb - Richard Kind is always awesome in everything he does and was great as Max Webb. Really liked the concept of the show within the show.
You Really Got a Hold of Me - Huge Dean Stockwell fan and loved the Quantum Leap tie in with his love interest being named Tina. Plus the foreshadowing of what Tom could become was well done.
Father - The closing shot of the photo behind the couch is one of my favorites from the whole show. Plus, Dean Norris in the dream sequence demanding the negatives was intense.
The Enemy Within - Probably one of Tom's biggest sacrifices. He could have been legitimately happy but in the end couldn't let go.
It's Not Such a Wonderful Life - If Nowhere Man had been a 12 episode mini series this would have been the perfect happy ending. But this was probably the Organization's BEST form of manipulation.
Hidden Agenda / Marathon/ Gemini - For the insight into the Organization.

The Enemy Within.
On the DVD Extras they spend a little time discussing this episode.
PS. I loved the DVD extras on this show.

My favorite episodes are "Paradise At Your Doorstep" and "Stay Tuned". I like almost every episode of this show though. The only one in the whole series that I found to be kind of dull was "The Incredible Derek".
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The best episodes for me would defintely be the last two episdoes it was very creepy to say the less but the most haunting and heartbreaking end for any character to handle. Also respect for the Pilot too that was pretty well executed you knew what sort of show this was going to be from the get go
Awesome show overall - would defintely cut 3-4 episdoes out to make the show more solid as they were just side stories that had nothing to do with the main plot - A solid 6.5/10 for me

A great one that no one has mentioned is the third episode, the one with the psychic kid.

Difficult to choose.
I loved "The Spider's Web", it was so suspenseful, yet also clever and tongue-in-cheek.
"Father" really resonated with me.
"The Dark Side of the Moon" managed to sneak in some social commentary.
"Calaway" gave us a look at the Organization's sinister inner workings.
I think my favorite would have to be episode 23 "Zero Minus Ten". This has got to be one of the creepiest and most suspenseful episodes, due to the simple fact that Tom's surroundings are outwardly normal. The irony here is that Tom gets what he has been striving for all season, his old life back, yet because of his experiences he can't enjoy it because he senses, correctly, that it's all a charade. The ending is just heartbreaking, worse than even episode 12's.

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I must confess that "Father" is my favorite because I got to watch several scenes being filmed in my hometown.
Unfortunately, it has yet to be listed in the "locations" credits (but I'm working on getting that fixed).
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Oh and how could I forget Through a Lens Darkly? That's a great one.

My fave (although it's hard to pick just one) is "Something About Her". Bruce and Carrie Ann Moss had such great chemistry!
Narrator of a life I'm reluctant to liveoffline!

It was on UPN, not FOX.

Hey Mike, I don't know how you first watched it on FOX, it ran here in Cleveland on UPN! My favorites are Father, & the episode where FBI Assistant Director Robman winds up getting shot by Jenny Shu, the FBI secretary Veil had rescued, insisting on NOT leaving her behind when they go to the photograph's site with her being controlled by "them", too

I've always like the Maria Bello episode.
What evil drives the Car?

Yeah, perhaps he should have suspected something, but come on he's got his gorgeous wife, it's Christmas Eve and everything is right in the world, and on top of that his estranged mother has come to make amends. What more could a man want? Even if you've seen it before, you want it to be true almost badly as he does
And of course Greenwood totally sells it. He really helped make the show great.
Yeah, Maria Bello looks great in that one. That's another good episode.

I remember watching the show during its first airing on FOX when I was in my teens. I recently bought the DVD set a tough chore here in Canada.
I am watching them again and just watched the christmas episode. I remeber this episode when it first aired and remember feeling quite upset that he wasn't "out there" and that he seemed to fall for it all so easily.
The episode before was nice to see Maria Bello in it, God she is so hot!

It's tough to pick my favorites because I feel like I'm shortchanging the series when I pick only a few. There are so many great episodes and only one or two I don't care much for.
That said, my favorite episodes are probably Absolute Zero, The Spider Webb and You Really Got a Hold on Me. Father and Paradise on Your Doorstep are great ones, too.