The former Caffe della Pace, cozy cafe on E. 7th Street. The kind of cafe that used to be quite common in lower Manhattan.
Siracusa was a nice Italian restaurant on Fourth Avenue north of Astor Place. White curtains on the window. Old-world service. Closed some time ago.
In the early '90s, as the East Village was gentrifying, Limbo, a cafe run by a group of Vassar grads, was a popular cafe for the pre-Starbuck's coffee set.
The Swiss restaurant Roettele A G on E. 7th, near Avenue A, was a popular haunt of mine in the early '90s, when I lived in the East Village. I've encountered few more charming restaurants in the City. I also had my first Beef Wellington there.