The Hidden Village of the Leaves (Japanese Romanization: Konohagakure), is the home village of the main protagonist, Naruto. It is also the village that is most frequenly seen throughout the series. Several of the village landmarks include the ninja academy, Ichiraku ramen. The ninja academy is the school for young children training to become ninjas; they are trained both physically and mentally to use ninja techniques and obtain the combat psyche required for a ninja. Ichiraku ramen is Naruto's favorite restaurant: a small noodle shop. Several important dialogues happen in this restaurant between Naruto and the other characters -- eventually signifying a deeper plot element in the story.
The Hidden Village of the Sand (Sunagakure) is the Leaf's primary ally since the end of the Konoha's destruction arc early on in the story. Gaara, the Sand village's current leader, is also one of Naruto's closest friends outside of the Leaf Village. The Sand village worked closely with the Leaf in several key missions -- including the Sasuke retrieval arc, where Gaara and his sibilings were instrumental to saving the lives of several main characters. In turn, Naruto also supported the Sand village in rescuing Gaara in the start of the Naruto Shippuden story.
The Hidden Village of the Rain (Kirigakure) is also the secret base of Akatsuki, the primary antagonist organization, made up of 12 rogue ninjas. Akatsuki's leader, Pain, is originally based from the Mist Village. In accordance with its name, it is almost constantly raining within the village. The architecture of the village reflects the system used to handle the rain -- using tools such as large metal pipes at the sides of each building to filter the water and avoid flooding the streets. The battle between Pain and Jiraiya, Naruto and Pain's teacher, happened in the Rain village; this battle resulted in Jiraiya's death, as his body sunk to the bottom of the Mist Village's artificial lake.
According to the storyline of the Naruto comics at the time of publication, two of the five great villages haven't been fully seen. These villages are the Hidden Village of the Cloud (Kumogakure) and the Hidden Village of the Rocks (Iwagakure). Other, smaller villages are featured only in the cartoons and movies based on the series and are usually considered separate from the canon story. These villages are usually introduced in short story arcs with new characters coming from these villages; however, these villages are only mentioned in passing, or not at all, during the rest of the story.