Ebony White, The Spirit's sidekick from the comics, was omitted, largely because he was typically portrayed as a 1930's racial stereotype. Frank Miller disliked the idea of The Spirit having a sidekick, so the character was completely removed, rather than updated.
There are several references to other comic book characters throughout the film: Sand Saref mentions Robin, Morgenstern mentions the Electra complex (based on the daughter of Agamemnon, the basis for the Marvel character Elektra), and The Spirit mentions Thor's hammer.
Stana Katic's character Morgenstern gets told twice: "You'll make detective in no time." and in the TV series Castle (2009), her character Kate Beckett is the youngest woman to ever make detective in the NYPD.