This isn't really a kaiju film, but its got so many strong ties to the genre, that I thought it more appropriate for this forum than the general sci-fi/horror/fantasy genre.
Tokyo! is an anthology film, similar to Scorsese/Coppola/Allen's New York Stories. It consists of three short films all centering around the city and the people who live in it, how the city affects them, how they affect the city, etc. Only, unlike New York Stories, this is much more of a surreal fantasy film, each movie being loaded with surreal dream logic and weird imagery. Each story kind of centers around the feeling of being isolated in a big city.
The first is called Interior Design, directed by the amazing Michel Gondry (Eternal Sunshine). The main tie to the genre here is that its lead character is Gamera star/Steven Seagal's daughter Ayako Fujitani. Its about a couple that moves to the big city and are staying with their friend. Fujitani's character feels that nobody appreciates her and she starts to turn into a chair.
The second is Merde, directed by Leos Carax. The big connection to the genre here is that this whole thing is in the monster movie formula. The movie's score is consisted ENTIRELY of Ifukube's Gojira score. The monster is actually a weird human with long fingernails and a beard in the shape of a spiral. He comes out of the sewer and causes all kinds of mischief in the city. He speaks his own language and he is taken to court. This one probably has the most symbolism and social commentary of the three. On the special features, the director said he'd never seen Gojira before and decided to watch it before doing the film because of its cultural significance. He watched it with his daughter and she loved the hell out of the movie and he said he found Godzilla to be a very sympathetic character and compared him to King Kong, Frankenstein, Mr Hyde, etc.
The third and final segment is Shaking Tokyo. The big connection here is that its directed by Bong Joon-Ho, who directed The Host. Its about a shut-in who refuses to have contact with anyone outside his house... he ends up falling for a cybernetic pizza delivery girl who he helps after being knocked out in an earthquake. He decides that he wants to go out in the world after meeting her, only to find that everyone in the city has decided to be how he used to be and not leave their homes.
Anyway, if you like surreal dream like films, or are a fan of any of these directors, or if you just wanna see some great stories about isolation in the city, I highly recommend Tokyo!.