12 Step Program to Organize your Movies

Download Ember here: http://sourceforge.net/projects/emm-r/
It doesn't require an install so you can place the folder wherever you want.
Once you have the application running set your media folder(s) by going to Edit>Tools.
Navigate to the "Files and Sources" tab under the "Movies" header.
Click the "Add Source" button and point it the folder containing your movies. Adjust any of the other options to preference.
While still on the "Files and Sources" page be sure to adjust the "Skip files less than" setting if you have any video files (like samples) with your movies that you don't want Ember to worry about.
You can adjust any of the other settings as you see fit, most are personal preferences dealing with naming conventions and info sources.
Close out of the settings and hit "Update Library" from the main window. This should populate the left column with your movies if it hasn't already.
Now click "Scrape Media" and go through to Moving Missing Items>Ask (Require Input If No Exact Match)> All Items. This process will take quite a while, especially if you have a large collection. You can do other stuff while this is going on, but be sure to check on it as it will prompt you for movies that it can't find. When it prompts just type the name of the movie in the search box and it will search based on that.
Once the scrape is complete be sure to go through and double check everything is correct.
To rename your movies with the new info go to Tools>Bulk Renamer.
Once renamed you'll want to make sure everything is sorted properly, do this by going to Tools>Sort Files Into Folders.

Your movies should now be properly identified, named, and sorted. This is really the tip of the iceberg of what you can do with Ember, but for now that's what I'm using it for. Once I have more time I'll dig deeper into the other settings.

UPDATE: Despite the website saying Ember supports TV shows it actually only supports movies currently. This will be expanded in new versions to include TV shows and possibly music.