I was recently working on SEO for a site when they decided to rework their structure and change all of their site to PHP. I have been working for the past 3 months or so building links to the .html forms of their files now though, which first had me worried. Then I remembered the 301 redirect and all of that stuff and how you can effectively let search engines know of page moves. Anyways, now that there is a redirect on the .html pages, should I still keep building links to the html pages, or to the new PHP pages?
Build links to the new PHP pages going forward. If possible I would configure the server to point to the directory and default the .php extension. Like this: http://www.yoursite.com/subfolder/ instead of http://www.yoursite.com/subfolder/index.html or http://www.yoursite.com/subfolder/index.php Then only build links to the directory structure instead of the file path. That way, any future changes with web extensions will not affect your ranking or PageRank.