I had to change my hosting option at Go Daddy from Windows to Linux. The problem I had was that I wanted to install and run PHP applications like WordPress, Joomla, and Magento (when available) in a more native environment and without any hacks. One of the problems, for example, is with WordPress in general and Permalinks specifically. I read a lot of hacks to do redirection in Windows and I didn’t want to do any of those. This not only affected the posts but also many installed plugins’ admin pages.
To switch your hosting account operating system follow these steps:
1) Select “Hosting” from the “My Products” menu.
2) Click the domain you wish to upgrade or downgrade.
3) Click on the ‘Upgrade/Downgrade Hosting Account’ link on the right
4) Follow the instructions to select the plan you require.
Go Daddy usually will take 24 hours to complete this change.
After completing this process, let me tell you that is a transparent transition. No issues were encountered. I had a sub domain setup that was not altered in any way. Neither of my installed application (WordPress and Joomla) were affected. No posts were lost. The only changes, of course, had to do with changing the IP address.
Once the process was completed, and the site was under Linux (basic plan) native support for permalinks was working. Remember that once you make and save your permalinks setting selection to let the changes take place for an hour or so.
Also remember that before making any changes to backup your data. Nothing beats peace of mind before clicking any buttons.
UPDATE (05/28/2009): I had to reinstall my WordPress app. I was not able to add images and all images appeared as broken links. Not sure if this was caused by the theme or the migration to Linux, but without time to find the answer it was easy to reinstall.