>>11396
Off the top of my head:
Muhammad Avdol from JoJo not outright stated but is an Egyptian
Mohamed Tabarsi from Shaman King also not outright stated but Shaman King is heavily influenced with religion
The Ishval people in Fullmetal Alchemist are pretty much a proxy of the Palestinians.
Yugo the Negotiator, haven't seen it myself but iirc, the main character actually recites al-Fatihah in one of the episodes.
The setting and main character of Magi is heavily based on the Arabian nights.
On how they're presented:
Avdol was one of the MC's companion and was popular enough that the author had to bring him back after he was killed by an enemy.
There aren't really "evil" guys in Shaman King. The plot is a bit complicated and Tabarsi was part of the "bad guys", per se, but he was still a decent person overall.
Scar is an Ishvalan Terrorist in FMA, but once you progress through the story, you find that a lot of his rage is justified and he become more of an anti-hero.
Magi is a pretty cheerful adventure manga, and a bit similar to Shaman King, people aren't necessarily "evil" and most who are have actual reason as to why they act that way.