This is something I always planned on doing but never got around to it. The realization that the site will be going away gave me motivation.
I'm gonna start with my personal top ten TV dramas, inspired by HBO rerunning The Sopranos this month to commemorate the 25th anniversary of the show's first airing.
These are my personal top ten. Two through ten are variable and can move up and down depending on my mood. Number one is carved in stone.
The Sopranos
The Wire
The Shield
House
Rescue Me
NYPD Blue
Justified
Ray Donovan
Hill Street Blues
Sons of Anarchy
Does the top two both being HBO dramas imply that you considered Oz and Deadwood and they didn't make the list? I've watched Sopranos and The Wire more than once each, but never Deadwood. I assume it would punch at that weight class, and plan to watch it some day. Oz is excellent, but most of the characters are worse people than even the characters in Sopranos or The Wire.
The West Wing probably belongs in this list. I would put it in my top ten, anyway.
I haven't seen anything on the bottom half of your list, and only a few episodes of House. I watched Rescue Me for a while, but thought it dropped off in quality and stopped before it ended. I would have Dexter in the list, despite that it also dropped off in quality.
I assume you'll have a different list for Sci Fi and Fantasy, so no need to consider things like X-files, Star Treks, Buffy, Firefly for this list?