All the Ochi's ones are good. Monday Motel, the Wednesday Faux Show, and the monthly Friday Virgin Mic.
Gutbucket at the UCB is the best, hands down, but it's not so easy getting on.
Superego at Ochi's is good too, it used to be at Parkside Lounge and was good there, but now the early show is at New York Comedy Club. I haven't been there since it moved.
I've heard good things about Bring It at the PIT but I haven't been to it. Also, there's a Maui Taco in midtown that has one in the basement every weeknight, but those are definitely hit-or-miss.
Let's start this thread back up! I'm looking for good mics. Also, check out
http://www.badslava.com, in my opinion the best New York open mic list (certainly the most up to date).