Are you aware of any file manager that is able to remember whether you want to show or hide hidden files for a specific directory? I.e. i never want to see hidden files in my home, but i would like to see them in all the other directories.
The Nautilus file manager for Ubuntu is capable of doing this on a per-folder basis:
If you want to see all hidden files in a folder, go to that folder and either click the view options button in the toolbar and pick Show Hidden Files, or press Ctrl+H. You will see all hidden files, along with regular files that are not hidden.