FFcoder is a wonderful piece of freeware capable of converting videos to nearly every conceivable format in existence. I use it frequently. The drag-and-drop interface is very useful. It's very easy to use for both regular users and advanced users. There's an plethora of extra features that come with it as well. The only caveat is the .NET Framework requirement. But it doesn't hurt to get it if you don't have it already.
You can download it here: FFCoder Website
Make sure to download and install the software listed under "Requirements" if you don't have them already. There's also a portable version available as well. It's also being actively developed and the developer responds to bug reports quickly.
I would just change the "File Format" drop-down selection to "Flash Video" and just drag-and-drop the videos into the window. Click the "Output" button to change the location of the converted files. Then, just hit start and wait for it to convert.