This is a very specific problem that applies to a small audience, but I recently had this problem that stumped the developers I was working with for a few days.
When you are changing your domain name for your Magento website, you will need to include redirects in the .htaccess file in the root of your website. But one important thing to know is that there are built in redirects for Magento that can get in the way of your server level redirects.
Magento is built with php and so every URL on your website looks something like /category/product-name/ or some variation. But the actual Magento URL is different so Magento has its own rewrites in the .htaccess file.
What you need to know is that if you are redirecting from one domain to another, you are doing server level rewrites. The default Magento redirects are application level rewrites.
Server level redirects need to be placed above the Magento application rewrites. The Linux administrator that was helping me at Rackspace informed me that this general rule applies to most applications.
If you are a Magento developer, and SEO specialist working with Magento developers, or a technical marketer dealing with this issue, this is something to look at if you are running into problems with a site migration.