MobileOrg needs to interact with Emacs through a directory on a server. If you
are using a public server, you should consider to encrypt the files that are
uploaded to the server. This can be done with Org mode 7.02 and with
MobileOrg 1.5 (iPhone version), and you need an openssl
installation on your system. To turn on encryption, set a password in
MobileOrg and, on the Emacs side, configure the variable
The easiest way to create that directory is to use a free Dropbox.com account2. When MobileOrg first connects to your Dropbox, it will create a directory MobileOrg inside the Dropbox. After the directory has been created, tell Emacs about it:
(setq org-mobile-directory "~/Dropbox/MobileOrg")
Org mode has commands to put files for MobileOrg into that directory, and to read captured notes from there.
 If you can safely store the
password in your Emacs setup, you might also want to configure
org-mobile-encryption-password. Please read the docstring of that
variable. Note that encryption will apply only to the contents of the
.org files. The file names themselves will remain visible.
 If you cannot use Dropbox, or if your version of MobileOrg does not support it, you can use a webdav server. For more information, check out the documentation of MobileOrg and also this FAQ entry.