With recent discussions about Freaks and Geeks I thought this would be a good discussion topic.
Here's my top 5:
Twin Peaks
First season is among the best I've seen. Second season is on the sketchier side.
Space: Above and Beyond
Created by James Wong/Glen Morgan who worked on X-Files. Similar plot to Starship Troopers but a lot stronger.
Carnivale
Moves pretty slow, but definitely worth watching if you can pay attention.
Jeremiah
Created by same guy who created Babylon 5. Very good concept. If you can get past the fact that Luke Perry, Malcolm Jamal Warner, and Sean Astin (S2) are in it, you'll see some brilliant sci-fi.
Firefly
A better version of Farscape.
Here's my top 5:
Twin Peaks
The body of a young girl (Laura Palmer) is washed up on a beach near the small Washington state town of Twin Peaks. FBI Special Agent Dale Cooper is called in to investigate her strange demise only to uncover a web of mystery that ultimately leads him deep into the heart of the surrounding woodland and his very own soul.
Space: Above and Beyond
In the years leading up to 2063, humanity has begun to colonize other planets. Suddenly, a previously unknown and mysterious alien species, the Chigs, attack and completely destroy two colonies. The bulk of the Earth military forces sent to confront the Chigs are destroyed or outflanked. In desperation, unproven and under-trained outfits like the 58th "Wildcards" are thrown against the Chigs.
Carnivale
During the American Great Depression in 1934, a great showdown between the forces of good and evil takes place, centered around hayseed Ben Hawkins and the sinister carnival with which he travels in the Midwest, and charismatic preacher Justin Crowe, who opens his arms to the migrant farmers arriving in California.
Jeremiah
In the year 2021, 15 years after a virus kills everyone over the age of puberty (both the event and the virus itself are referred to as "The Big Death"), the child survivors have grown up, living on the scraps of the old world.
Firefly
Five hundred years in the future, a renegade crew aboard a small, mobile, spacecraft tries to survive as they travel the unknown parts of the galaxy and evade warring factions as well as authority agents out to get them.