In what order should I read the Touhou Project manga? After a little online search, I've found the following list, compiled from wikia and wiki (excluding the two short stories and including the two comics in the Artbooks section), of official Touhou Project manga related to ZUN's scenarios:


Eastern and Little Nature Deity
Strange and Bright Nature Deity
Oriental Sacred Place
Extra of the Wind
Memorizable Gensokyo
Silent Sinner in Blue
Inaba of the Moon and Inaba of the Earth
Wild and Horned Hermit
Forbidden Scrollery


In what order should I start reading these manga?
I heavily recommend reading the manga in release order, taking into consideration the release dates and plots of the official games. Most of the manga are standalone (with some exceptions) in the same way that the games are standalone to an extent, but keeping everything in line with game release dates will allow for better understanding of the plot context. 

Note that the manga focusing on the three fairies are directly associated with the Great Fairy Wars game, and note that Kasen did not have her first appearance in a game until WaHH had been going on for quite a while.

In general however, feel free to read them in any order (aside from the ones that are direct sequels, etc). Inaba of the Moon and Inaba of the Earth for example is entirely made up of separate comics, and as long as you are familiar with the dynamic of the characters, it is an enjoyable experience.