Athens has a variety of good restaurants. They can be found in places where the locals go, not at the tourist areas, which are full of tourist traps and fake greek cuisine presenting souvlaki and mousaka as the dishes of the greek kitchen. Greek cuisine has thousands of dishes and is a healthy cuisine with mediterenean colour and taste and base the olive oil.
For people not familiar with Greek dining, here are some practices one should be aware of: (1) Bread basket is not free, usually €1-2. (2) Typically all taxes and service charge are included in the menu pricing. But you may add tips on your own. (3) House wine by the half liter usually is decent quality and costs €6-8. If you have finicky taste, order the white instead of red. (4) Do not expect sides such as veggies or potato on the entree dish, unless the menu describes them. (5) Most local dishes are small plate style, costing under €10. Grilled or fried food is very popular and very local. (6) Local menu usually does not distinguish between fishes, except salmon. Most fishes are called white fish, whether big ones like cod or small ones like sardine. (7) Tap water in Athen restaurants is drinkable, even in small mom & pop places. (8) Real local eateries have small interior space, but by dinner time, they add more tables on the sidewalk. Be prepared to dine outdoor in the elements and under street lights. Many outstanding foods are served in minimum decor or ambience. (9) Local joints seldom take credit card. When they give you back cash changes, don't be surprised if they round off the dimes/cents and give you more back!
Nice greek restaurants that presenting a pice of that cuisine are:

Delfino Restaurant (20-40€) Delicious seafod and fresh fish by the sea.
Filistron (20-25€)
Istioploikos Mediterranean Cuisine
Ochre & Brown BaRestaurant (40-50 €) Fine Modern Greek and Mediterranean Cuisine.
Varoulko (80€). Greek gourmet sea food cuisine; Michelin star.
Other great restaurants of the city, with awards and Michelin stars(the highest honor of a european restaurant):
Spondi (100€)
Jerome Serres Self-named restaurant by the former chef of Spondi, located next to Varoulko; also with a Michelin star.
St'Astra at the Park Hotel. Nice views of Acropolis and Lycabettus.
Edodi (60€)
Thalatta (30-40€). Greek sea food cuisine
Orizontes Lycabetous (80€) on Lycabetous Hill
Alexander the Great Restaurant Authentic Greek Traditional Cuisine
A very nice guide if you understand Greek is Athinorama with its gourmet awards.
All these are restaurants can satisfy you in Athens, and they are places where the locals go, too. It's hard to believe that so many of the nice restaurants of Athens are outside of the tourist areas. More can be found Gazi, Kolonaki and hidden in streets of Psiri.
