Prune - very quirky with a Dutch pancake, deep fried Monte Cristo, fruit juice blend called "prune" juice, oysters & sausage, "hostel" style breakfast. Also eclectic.
Tasting Room (not EV but very close if you live by Houston/Bowery edge, is in Nolita) - very seasonal/localvore, menu changes all the time, great duck rillettes, they have unusual treatments of the typical pancakes and waffles (like unusual grains or additions). A bit on the healthy side. Try the bloody mary made with red wine.
The Smith - some items on there have a southern twist, which is refreshing
5 Points - lemon ricotta pancakes, bourbon vanilla french toast, egg dishes are typically baked in a skillet in their wood burning oven
Belcourt - eclectic menu, ex-Prune chef, they have salt cod hash, English breakfast, boudin noir
EU - really nice, big room, try the Belgian waffles or hunter's breakfast, charcuterie plate, burger with an egg on top
Caffe Emilia - breakfast done Italian style mostly egg stuff and panini, like Taralluci e Vino or 'ino/'inoteca, but done very well)
Cafe Mogador - some middle eastern dishes on the menu
Veselka - blintzes, periogi, good, cheap, crowded
La Palapa - inexpensive pre fixe that comes with a drink, Mexican-influenced french toast and all that
Back Forty - haven't been yet but been hearing a lot about their donuts, am eager to try their fried chicken and waffles dish
TECHNICALLY LES OPTIONS
Stanton Social (technically LES as it is south of Houston) - great atmosphere, nice donuts, ricotta fritters, chocolate pancakes, mac and cheese, fruit quesadilla with bacon, etc. Eclectic
Spitzer's Corner (ditto) - I believe Wayne Nish just revamped the menu, there are interesting burgers on there, pork benedicts, foie gras mousse-stuffed dates, herbed popcorn, haven't tried this yet
Alias (not sure who the new chef is) - breakfast burritos, I think they might still serve goedda, fried chicken and waffles
Shopsin's - almost the definition of "not your usual brunch"!