Sharepoint - How to fix "Missing server side dependencies"

I was able to fix this by removing the old versions of the page that referenced the web part. I restored version 1 created by the system account. Then it gave me a warning saying that it didn't use the right template and I needed to click okay to fix it. After that, I went into page history, versioning, and removed all the older versions. Then I went into the recycle bin and deleted them. Then I went into the site collection recycle bin and permanently deleted them.

You might be able to track down the old references using SharePoint Manager from CodePlex: http://spm.codeplex.com/

Make sure you use a FeatureReceiver when deploying Master pages and use the FeatureDeactivating event to clean up after yourself. SharePoint won't remove these things for you because it doesn't know if you're done with them and doesn't want orphans.

It's been my experience that Missing server side dependencies are the result of solutions that are improperly retracted, amongst other things; but for the most part.

Check out my blog post that describes one semi-non-envasive approach to resolving this: http://anothersharepointblog.com/missing-server-side-dependencies-reference

Also: take a look at the get-spscripts site's information on this topic, I've found it to be the best resource: http://get-spscripts.com/2011/06/removing-features-from-content-database.html