Here's a list of the titles, accompanied by a link to the article. The full article includes cover images, and short summaries of each comic with the publisher/creator information include.
Quick note, I fixed the Yotsuba&! creator credit.
Quote:
Publishers Weekly's Best Comics of 2005
Epileptic by David B. (Pantheon)
Ex-Machina: The First Hundred Days by Brian Vaughan and Tony Harris (DC/Vertigo)
The Rabbi's Cat by Joann Sfar (Pantheon)
Scott Pilgrim vs. The World by Bryan Lee O'Malley (Oni Press)
Ghost in the Shell 2: Man-Machine Interface by Shirow Masamune (Dark Horse)
WE3 by Grant Morrison and Frank Quitely (Vertigo)
Black Hole by Charles Burns (Pantheon)
King by Ho Che Anderson (Fantagraphics)
MBQ vol. 1 by Felipe Smith (Tokyopop)
The Genshiken vol. 1 by Kio Shimoku (Del Rey)
Gemma Bovery by Posey Simmonds (Pantheon)
Teenagers from Mars by Rick Spears and Rob G. (Gigantic Graphic Novels)
Why Are You Doing This by Jason (Fantagraphics)
Yotsuba&! by Kiyohiko Azuma (ADV Manga)
Walt and Skeezix : Book One by Frank King (Drawn & Quarterly)
Salamander Dream by Hope Larsen (AdHouse Books)
Tricked by Alex Robinson (Top Shelf)
Night Fisher by R. Kikuo Johnson (Fantagraphics)
Dramacon by Svetlana Chmakova (Tokyopop)
Astonishing X-Men Volume 1: Gifted by Joss Whedon and John Cassaday (Marvel)
Street Angel by Jim Rugg and Brian Marucca (Slave Labor Graphics)
Epileptic by David B. (Pantheon)
Ex-Machina: The First Hundred Days by Brian Vaughan and Tony Harris (DC/Vertigo)
The Rabbi's Cat by Joann Sfar (Pantheon)
Scott Pilgrim vs. The World by Bryan Lee O'Malley (Oni Press)
Ghost in the Shell 2: Man-Machine Interface by Shirow Masamune (Dark Horse)
WE3 by Grant Morrison and Frank Quitely (Vertigo)
Black Hole by Charles Burns (Pantheon)
King by Ho Che Anderson (Fantagraphics)
MBQ vol. 1 by Felipe Smith (Tokyopop)
The Genshiken vol. 1 by Kio Shimoku (Del Rey)
Gemma Bovery by Posey Simmonds (Pantheon)
Teenagers from Mars by Rick Spears and Rob G. (Gigantic Graphic Novels)
Why Are You Doing This by Jason (Fantagraphics)
Yotsuba&! by Kiyohiko Azuma (ADV Manga)
Walt and Skeezix : Book One by Frank King (Drawn & Quarterly)
Salamander Dream by Hope Larsen (AdHouse Books)
Tricked by Alex Robinson (Top Shelf)
Night Fisher by R. Kikuo Johnson (Fantagraphics)
Dramacon by Svetlana Chmakova (Tokyopop)
Astonishing X-Men Volume 1: Gifted by Joss Whedon and John Cassaday (Marvel)
Street Angel by Jim Rugg and Brian Marucca (Slave Labor Graphics)