Suppose you have an old legacy website, with an in-house php CMS.
http://mysite.com/index.php?page=3&c=7
Now, for some reason, you re-structured your website in Wordpress, with SEO friendly URL's, registered a Google Analytics account, and needs to update your system, so when
http://mysite.com/
is set on the browser, now it points out to your new installed system.
The problem is that your website is old and already well know by your clients. A lot of people have bookmarked a lot of links in your webpage, so just redirecting your domain for your "new website" would create a bunch of broken links or other problems relative to SEO.
So, in this scenario, which steps should you take when doing this shift? (I can only remember of using mod_rewrite in a lot of complex schemes). Are there other "best practices" when you change systems in such a way that you lose all your old links?