If you're looking for manga similar to Shakugan no Shana: Shana & Yuuji no Naze Nani Shana! Nandemo Shitsumonbako!, you might like these titles.
An official gag comic for the TV anime, "KIZNAIVER" appears! In this gag comic, all of the "KIZNAIVER" characters have turned mini, and live out unbelievable days in Sugomori City. You get to enjoy a slightly different story from the original.
Yu-Gi-Oh! D Team ZEXAL focuses on humor and all characters are drawn in a chibi style. Different from the canon series, aimed at juvenlies, this manga series is aimed at younger children, and teaches them how to play the Yu-Gi-Oh! OCG with a light and humorous plot.
Another version of the story of the Inspectors and Enforcers from Psycho-Pass, but this time in chibi style! All of the main characters are now in chibi form, and are attending a "Psycho-Pass Academy," which is basically a chibi-fied version of the scenario of the original series. New student Tsunemori and her classmates will use their Dominators to keep their school's peace!