Here's how to do it for Ubuntu:
Write to file /usr/local/share/applications/emacsclient.desktop:
[Desktop Entry]
Name=Emacsclient
GenericName=Text Editor
Comment=View and edit files
MimeType=text/english;text/plain;text/x-makefile;text/x-c++hdr;text/x-c++src;text/x-chdr;text/x-csrc;text/x-java;text/x-moc;text/x-pascal;text/x-tcl;text/x-tex;application/x-shellscript;text/x-c;text/x-c++;
Exec=/usr/local/bin/emacsclient %F
Icon=emacs
Type=Application
Terminal=false
Categories=Development;TextEditor;
StartupWMClass=Emacs
Just make sure that emacsclient is indeed located in /usr/local/bin/emacsclient
(you can use which emacsclient in bash to see this).
Then execute from bash:
sudo update-desktop-database
Finally, add to your ~/.emacs:
(require 'server)
(or (server-running-p) (server-start))
After this, once an Emacs instance is running, clicking on a file in Nautilus
will open it in the current window of Emacs, without changing the window configuration.