I would say that my favorite place would have to be Little Giant on Broome & Orchard. It's small, and the menu is not robust but it's one of those places that you cannot get a bad meal at! Plus they have a keen eye for wines from vineyards that you may not know about but will definitely like. Oh and if they have the ginger mojito available get it! My definite recommendation!
Try Pommes Frittes it's on second ave and seventh. It's just French fries but there good French fries. Right across the street is San Loco. Like there chilli.
I sometimes work near 2nd & B. Two good, affordable lunch spots are the vegetarian Indian cabbie joint (named Punjabi Deli, I think?) near the northwest corner of Avenue A & Houston.... and also Cafe Himalaya, near the northeast corner of 1st & 1st.
Schillers is pretty great. But don't be confused by the bathrooms, the big trough in the first room is for washing your hands. You have to continue on to the second room to pee.