This patch should solve feature request 2966770 (https://sourceforge.net/tracker/index.php?func=detail&aid=2966770&group_id=153444&atid=787794), i.e. it should enable opening remote files via drag and drop from Nautilus.
It works for me with Geany 0.20 on Debian stable x64 with Gnome 1:2.30+7 / Nautilus 2.30.1-2squeeze1. I don't know about other configurations.
Let me know if any other information is needed.