The Huffington Post has a list of the 10 most popular graphic novels that have been challenged in libraries. The list purports to be from the American Library Association, but I can't find it on their site; I suspect they pulled the graphic novels off several lists of challenged books. Here they are:
• Absolute Sandman, by Neil Gaiman and others• Blankets, by Craig Thompson• Bone, by Jeff Smith• Fun Home, by Alison Bechdel• Maus, by Art Spiegelman• Pride of Baghdad, by Brian K. Vaughan and Niko Henrichon• Tank Girl, by Jamie Hewlett and Alan Martin• The Dark Knight Strikes Again, by Frank Miller and Lynn Varley• The League of Extraordinary Gentlemen: The Black Dossier, by Alan Moore and Kevin O'Neill• Watchmen, by Alan Moore and Dave Gibbons
Notably absent from the list is any mention of manga, which has been challenged in several libraries recently.