I use GoDaddy's unlimited/ultimate hosting account for the Windows OS. I have multiple domains hosted under this plan. For each domain I created a subdirectory with the name of the domain and pointed (aliased) the domain to the similarly named subdirectory (i.e., "domain1.com" is aliased to "\domain1com", "domain2.net" is aliased to "\domain2net", etc.).
I performed an Application Install of WordPress for each domain. NOTE: the install script will only allow the selection of the hosting account's Primary domain. This is OK, this will be corrected in a later step. For the installation directory I specified the desired domain name subdirectory followed by "\wordpress" (i.e., "domain1.com" is installed in "\domain1com\wordpress", "domain2.net" is installed in "\domain2net\wordpress", etc.).
If your primary domain is a functional (i.e., registered NOTE: mine is not) you should be able to navigate to "primarydomain.com/domain1com/wordpress", go to the Settings - General page, and modify the two links changing "primarydomain.com/domain1com" to "domain1.com" and repeat for each install. If the primary domain is not functional, you can use the database manager to oprn the various databases and change the entries. Unless you do this step, NONE of the links generated by WordPress will work.
If you have to modify the database directly, perform the following: After I am finished with the installs, I examine the installation details to determine the databasename created for each installation. I use the database manager to open each database and browse "wp_options". You will find two entries which contain the directories WordPress will use when building links to access objects within the installation. By default, the hosting account's Primary domain is specified at the beginning of the link, followed by the installation directory path specified during the install (e.g., "http://primarydomain.com/domain1com/wordpress". I modifed the entries to have the "correct" domains (e.g., "http://domain1.com/wordpress" NOTE: the matching subdirectory name is not needed since the corrected domain is already aliased to it.). Logout of the database. Repeat these two modifications for each domain's database.
Now, I can successfully navigate to "domain1.com/wordpress", WordPress runs, and ALL links are functional. I have not encountered any other problems with GoDaddy's WordPress installation to-date. If there are any problems I can "expect" to find, I would appreciate anyone giving me a heads-up.