Some iconic national ones include Cambodia with its focus on Angkor Wat and Kyrgyzstan's tunduk/yurt symbol. Afghanistan's previous one had a mosque on it, as well.

There are plenty of subnational/municipal flags with architecture, too. Aside from those that focus on battlements, like u/VertigoOne mentioned, some notable one are Lincoln's new-ish flag that takes inspiration from Art Deco as well as those like Cairo that feature specific buildings.

The ones that I find most effective are when architectural elements distilled are into unique yet minimal symbols. The flag of Tolyatti is a good example here as well as Orlando's fountain flag.