You can use Compressor. You’ll just have to tweak the frame controls until you’re satisfied with the results.
There’s no magic bullet fix or 1, 2, 3 process. It depends on the originating camera, codec, type of footage, and what you’re willing to accept. The image will likely be a bit softer as you’re either combining fields or you’re throwing one way and interpolating between the two.
I would get a sample file (30 seconds long or so) and use that to test out several different settings. Assuming you have a lot to do, find the setting you like best based off your sample clip and then run all your footage through in a batch overnight. Depending on the settings you can choose it can take close to realtime or up to 5 to 10 times realtime (based largely on what setting you choose for “Motion Estimation”). Remember this process is very computationally heavy. So leave yourself plenty of time to test and transcode.
Ryan Holmes
http://www.ryanholmes.me
vimeo.com/ryanholmes