If we limit it to midnight to 5am, I would say NBC’s Poker after Dark is rather watchable. Anything after 5am is a morning show.
Probably Family Guy re-runs on Adult Swim. Years back, I would have said anything on Adult Swim, but a good portion of their original programming is unwatchable now.
I like Hold 'em, but Poker After Dark is too slow and cut up with way too many commercials. I can barely stand listening to the players endlessly futz with their chips. So annoying! I much prefer watching tournaments that table hop and show lots of hands.
Red Eye on Fox News Channel, at 3 am (2 am central). Hilarity. It’s like the McLaughlin Group, but on crack.
Craig Ferguson seems to have quite a strong following. Though it actually airs before midnight in the Central Time Zone.
I can always find Seinfeld, Frasier, King of the Hill, or Family Guy on after midnight.
The Venture Brothers is still good…I’m not sure if it airs after midnight though. Metalocalypse is also good. Robot Chicken is hit-or-miss, but I like it enough to keep it on the TiVo. But I agree with you…most of the new programs they have introduced are absolutely horrible.
Scrubs is borderline 24/7 these days…
Adult Swim is nice
NFL network is usually watchable at all hours (if you like football)
ESPN
or, there are the two obvious choices - DVR and Watch Instantly 
That’s what I came in to say - he’s damned entertaining, and we see a lot of good new music on his show as well.
I haven’t seen it in awhile, and it tends to be preempted by local stations, but ABC World News Now used to be must-see TV for the late-late-late night crowd. How many news shows have ever had their own polka, AND gotten William Shatner to sing it live in the middle of the night.
Yeah I really like Venture Bros. too, though the last season felt really off and nowhere near as funny, in my view.
I don’t like Metalocalypse, but I don’t think it is bad - just not for me. Tim and Eric is a bad show.
Craig Ferguson. I catch up on the previous night’s show every day during my lunch break.
I wouldn’t call it the “best”, but sometime around 2:30 AM I accidentally caught a show on IFC called Food Party and laughed my ass off. It’s surreal and insane and amateurish, and I don’t really know what to make of it. But I’m still watching.
Seriously? That’s still on?
The “sit on you” song and dance is sorta funny; also, one episode made a reference to a community college near my very, very rural hometown (in that context, I found it amusing). Other than that, there’s not much to see. Tom Goes to the Mayor is even worse though.
My after midnight viewing is usually the late rebroadcasts of Daily Show and Colbert, Anderson Cooper, and if the others aren’t watchable- I’ll admit it- The Nanny reruns.
PBS often rebroadcasts shows from earlier in the week. I was kicking myself when I came across a rebroadcast of the Lincoln Center production of South Pacific at 2 a.m. after missing it earlier in the week.
Not much to choose from, but Craig Ferguson is the best thing on that starts past Midnight.
He’s quite funny.