In the West Village, I like
Pink Teacup, although there's generally a line. In Tribeca, there's
Kitchenette (the website is out of date and they've recently moved around the corner to Chambers St. between W. Bway and Greenwich).
For Upper Westside options, there's Good Enough to Eat (site of a previous FT gettogether), Sarabeth's, Popover Cafe, Barney Greengrass...
Have never done Norma's in the Parker Meridien--it's very popular, but it sounds like an overpriced scene to me.
And while it's not in Manhattan, I'm now in love with
Egg. It turns into a different restaurant from noon, though, so you have to get there early.