A Few Faves:
Toms Diner (Really kind of the best. Tough to top it.)
Jimmys Diner (Great menu items that don't exist anywhere else. Key Lime Pie Milkshake with an actual slice of Key Lime Pie IN the shake!)
Acapulco (Mexican Diner in Greenpoint. I just have a soft spot for it.)
Grand Morelos (Mexican Diner that is open 24 hours. Great 4AM torta.)
Diner / Relish (Fancy shithole Williamsburg diners. Heirloom Tomato Salads, Macaroni and Cheese, Veggie burgers and Kentucky Milkshakes)
Some Cuban Diner on Vanderbilt and Bergan (Great Cuban Sandwich, and other Cuban delights.)