I have found that in the gnome-control-center if I want to make it so that a folder does not come up in search and I go to the "Search" section if I click on the options menu which launches up "Search Locations", click the "+" button, select the folder and then press the slider to turn it "Off" it disappears from the list, in fact anything in the "Other" section does, even "Desktop" which is there by default, though adding an item back to the list where its status is "On" makes search results be displayed for it again. I am running Ubuntu GNOME 15.10 with GNOME 3.18.

I think it would be better if there was a different system where you have the folders in "Places" where they are now, but then instead of having the "Other" section (and "Desktop" should be in "Places" and not "Other") there should just be a blacklist to which you can add folders if you want (obviously adding a folder which is one of those in the "Places" list will simply disable it in "Places").

I initially reported this issue here but thought I should also do so upstream: https://bugs.launchpad.net/ubuntu/+source/gnome-control-center/+bug/1575941