1) Flat. So if its in a zip I can see the folder structure and what the mod has be it textures, meshes etc. As a modder I like to know these things. Sometimes I've downloaded a mod that sounded like it had some nice models in it but up inspection of the folder structure I have seen no meshes folder and thus anything in the mod would have been made from either vanilla meshes or another mods meshes.
2) In the Data FIles folder. This is becasue if you're in there you're generally looking for resources and you'll have to jump an extra level if their in the exe folder. Plus people should generally be kept out of the folder that the exe is in.
3) readme_modname.txt. Only because when you're browsing through a folder with a lot of files its good to group files as well as possible and if you're looking for a readme its easy just to hit the "r" key and get straight there. Plus sometimes modders don't call their call their mods by the same name through the mod. This has made it hard to find readmes sometimes.
4) "Readme etc". Only because I like how it flows. Just seems right.