That depends on what you are going to do with those video files.
If your goal is further editing, any compression is futile, as iMovie needs HD video to use the .mov container with the Apple Intermediate Codec (AIC -
KB by Apple on storage consumption to make editing possible.
If you just want to archive the video, it is best to use the original files from your camcorder, as those files have already been transcoded during the import into iMovie. Another transcoding process (compressing it) will only loose you image quality (visible and other information).
If you just want to save the finished sequence (the movie you made with iMovie), then you have to decide, which format and resolution to use.
.mov and .mp4 files are only containers for a variety of codecs, the most prominent being the H264 codec, which is a popular and quite excellent variant of the MPEG-4 codec.
So in order for us to determine, what might be the best option for you, you need to give us further information.
What exactly and to what purpose to you want to compress, and what specific camera model are you using?