You just need to unzip the extension in the ~/.local/share/gnome-shell/extensions folder and rename the extracted folder according to the UUID declared in the metadata.json file.

Eg : You want to install topicons, from From the extension homepage, you can find the latest version source (as of may 2015) :

% cd ~/.local/share/gnome-shell/extensions
% wget
% unzip
# you can edit and check the extension
% grep uuid topicons-26//metadata.json
  "uuid": "",
% mv topicons-26

You should now be able to enable the extension from gnome-shell-extension-prefs.
If the extension does not show up as it happened with me, you should try to reload gnome-shell (alt+F2, r, then enter).