The Girl From H.O.P.P.E.R.S. by Jaime Hernandez (Fantagraphics, $20). These beautifully drawn stories feature some of the most believable, diverse, and indelible characters in the history of comics. "The Return of Ray D." and "Spring 1982" changed my life, and are still among my favorite short stories in any medium.
RAW edited by Art Spiegelman and Françoise Mouly (out of print). Including this anthology is a bit of a cheat, since the work in it ranges across various formats, but this book gave me my introduction to international comics, art comics, and comics as literary short stories. It's arguably the most significant compendium of modern cartooning, and certainly the one that most deserves republication.
My New York Diary by Julie Doucet (Drawn and Quarterly, $17). This is a collection of bracingly honest and unsentimental stories about the artist's teen years and brief residence in New York City. As with all the best comics, the drawing and writing are completely inextricable, and even the most mundane moments are transformed by Doucet's style.
Rusty Brown by Chris Ware. This serial about a bullied schoolboy who seeks solace by collecting toys hasn't been completed yet, but four chapters have been published as part of Ware's Acme Novelty Library series, and those are already more than sufficient justification for the work's appearance on this list. The stories contained in Acme's volume 19, in particular, are a high-water mark for both comics and fiction.
Abandon the Old in Tokyo by Yoshihiro Tatsumi (Drawn and Quarterly, $17). Originally published in 1970 in Japan, this collection of stories veers wildly between outrageous melodrama and delicate quotidian observation. The book is a furious examination of the lingering aftershocks of war and the side effects of the country's "high-growth" economic period.
Caricature by Daniel Clowes (Fantagraphics, $17). I wish every one of my favorite cartoonists would produce a version of this book: a handful of short stories, all distinct in style, yet all unified by the artist's singular sensibility. A master class in concision and characterization, with seemingly endless tectonic layers of implication.