How can I efficiently convert MOV / MPEG-4 files for long term storage?
Although @stib's advice is sound, I disagree with "to get an appreciable size reduction you would have to throw away a lot of quality". Cameras have to compress on-the-fly, so they use constrained baseline mode, which is to say, they skip most of the tricks that H.264 codec uses to efficiently compress videos. If space isn't a pressing concern, keep them as-is. But if you'd like to recover some space, you can use ffmpeg, a command-line tool, to compress them while generally retaining quality.

ffmpeg -i input.mov -c:v libx264 -crf 12 -c:a copy -c:d copy -map 0 compressed.mov


CRF values in the range of 12 to 15 will give you a smaller video stream, generally by 25 to 40%. Perversely, if your scene has a lot of fine texture detail like a forest or pebbles or embroidered cloth..etc, then compressibility won't be high and using these CRF values will likely produce output which is larger than the source. Skip compression in these cases. For most scenes, filled with smooth gradients or nearly-flat shaded surfaces, compression should yield a smaller file with good quality.