Really cool Totoro, I'm digging this.
Being a fan of cable/premium programming, I'd consider...
From HBO
-Would Oz make the cut? It started in '97, 2 years before The Sopranos/The West Wing and 32/56 of its episodes did air in 00's.
-I second the including of Deadwood.
-Tell Me You Love Me- Sadly only ran for one season, but was very acclaimed and controversial in its startling realistic depiction of sex. Had a great cast too.
-John from Cincinatti- Also ran for only one season. Despite an incredible cast and created by David Milch (Deadwood, Luck), I wasn't all that crazy about it. I think a few fellow Filmspotters were fans.
-Hung- I was a fan. Pilot was directed by Alexander Payne, starred Thomas Jane, created by Dmitry Lipkin (wrote the FX series The Riches) and ran for three seasons. I think it goes alongside Bored to Death and Eastbound and Down. They all came out around the same time IIRC.
-Luck- Another Milch show that only ran for one season. Amazing cast and a pilot directed by Michael Mann.
-The Newsroom- A show from Aaron Sorkin and starring Jeff Daniels. Very topical and will be concluding this year with its third season.
Showtime
-Brotherhood- Ran for three seasons. Fantastic crime show about an Irish family with connections in crime and politics. Starred Jason Isaacs and Jason Clarke. I'm a little biased as I'm a huge fan of those two actors.
-Sleeper Cell- Only ran for two seasons. Had a great ensemble and I considered it to be of a much higher quality than say 24.
-Dead Like Me- Ran for two seasons and created by Bryan Fuller (Pushing Daisies, Hannibal). Great cast and phenomenal writing. Has some Filmspotting fans I believe.
-Huff- I actually haven't seen this. Comedy that ran for two seasons starring Hank Azaria, Blythe Danner, and Oliver Platt. It was nominated for many awards I believe.
-United States of Tara- Ran for three seasons. Created by Diablo Cody and starred Toni Collette who gave such an incredible performance.
FX
-I also second the including of The Americans. Such a complex and layered show.
-Might as well include The Bridge. It's along the lines of The Killing and Hannibal (and was on Abed's DVR in that Community episode about the Ass-Crack Bandit this season).
-Over There- I didn't watch this and I've heard incredibly mixed things about it. It was a series about soldiers overseas in the Middle East and did receive some criticism for the show being heavily anti-war. It was executive produced by Steven Bochco.
-Thief- Great crime series starring Andre Braugher that FX called a miniseries at the last minute when they cancelled it and wanted to have it compete in awards season (Braugher did win an award for it, forget if it was the Emmy or Globe).
-Dirt- Like Over There, I've never seen this, but it ran for two seasons. Starred Courteney Cox as head of some of gossip magazine and was created by Matthew Carnahan (House of Lies).
-The Riches- I was a huge fan of this show about a family of grifters. Created by Dmitry Lipkin (Hung) and starred Eddie Izzard and Minnie Driver as the main characters.
-Terriers and Lights Out- Two shows that came out around the same time. I think both have some fans. I'd heavily campaign for the inclusion of these. Crime-related shows about a P.I. and a boxer respectively. Dark stories with great performances (Donal Logue and Holt McCallany respectively).
-Wilfred- Very funny show starring Elijah Wood as a man who can talk to his neighbor's dog that is played by Jason Gann as a guy in a giant fuzzy dog suit.
Starz
-Shows with high production values include Da Vinci's Demons, Black Sails, Camelot, Magic City (looks to have a great cast), and White Queen. Haven't seen all that much of any of those.
-Boss- Kelsey Grammer got some acclaim being cast against type as a corrupt mayor. It had a great ensemble despite sometimes just being too messed up for its own good.
AMC- I really liked Low Winter Sun. A crime show with Mark Strong and Lennie James. I might be the minority on that.
Netflix- Orange is the New Black. Also if we are including some other Gervais shows, I think Derek fits in nicely with respect to his past work.
Sundance has two shows called Rectify and Red Road. I loved Rectify. A show with plots that seem to boil but have an amazing amount of complex emotions involved.
A&E has Bates Motel which has a good following.
The West Wing, Alias, and Pushing Daisies are some network series that come to mind as well. Also, should you include miniseries/TV movies because in that case Band of Brothers, Angels in America, and many others come to mind.