Saved! and Dangerous Lives of Altar Boys are both awesome, and both star Jena Malone (love herrrr).
Saved! is the story of a girl in a very prepster and religious type high school who finds out her boyfriend is gay, so she attempts to "save" him, getting pregnant in the process. Patrick Fugit is also in this one! And it's more of a satire than anything else really, and it's less dark.
Dangerous Lives of Altar Boys is older and much darker than Saved!. In this, a group of boys have rad adventures and draw comics. They also go to a religious school and they hate on a nun played by Jodie Foster. One time they try to kidnap a mountain lion from the zoo!
Chumscrubber is another one that is awesome, but this one is much more dark than comedy, but still very good and still very funny (just in a twisted way).