When I decided to do mod_rewrite on all of my site links to be a little more friendly ( 300 ) indexed pages, I basically did the above for the old .php indexed pages. I also threw in the robots.txt all of the old page links, which is stated by Google for removing urls or pages. Once Google recognized that the pages were on the new URL's the .php pages starting dropping off. I suffered no duplicate content penalty. This was a month ago I started this process, now I have over 600 indexed pages by google, impressions have increased by 13k. As long as you follow all best practices, you should be fine. Just make sure you you do whatever you can to provent duplicate data penalty, example, same content on two different domain names. robots.txt will remedy that in a short time. do site: proxyfreak.org and you will see a few .php pages left, but my keyword rankings and impressions were worth the change.