I agree with Ort. about Pilgreen's. Thanks to his recommendation, Jane and I were lucky enough to eat there one time, and it was a classic in every way.
Personally, I miss the old Jimmie's of Savin Rock (Connecticut) where the hot lobster rolls were ultra-buttery, the split weiners were crisp, and the countermen were like Marine D.I.s on crystal meth. Another New Haven area place dear to my heart is the old George & Harry's, an ancient Greek-run cafeteria/tavern with spectacular carved woodwork everywhere.
Also, two other long-gone greats in Georgia: Mrs. Bonner's of Crawfordville, for the greatest sweet potato pie; and CH Mitchell the Bar B Que King for BBQ and Brunswick stew.
Then there's the chicken at Mary's Cupboard in Winnetka, Illinois ... and the world's best hot fudge sundae at The Sweet Shop, also in Winnetka (my home town) ... and
... oh, this is too sad...