Start by explaining where you want these files to go, how they are to be viewed and how you are justifying the need for color accuracy since you have no control over the setup of the playback monitor, in most cases. Your output issues from FCP sound like user settings problems. There is nothing inherent in FCP that would cause your image to change that much. However, transcoding between color spaces is tricky and requires careful control over the production pipeline from exposure to output.
H.264 is simply a codec; you can use it from within almost any Quicktime exporting tool. Batch exporting using Compressor is remarkably easy to set up and even automate. Using 264 on DV is only a valid choice if you need 264’s unique scalability properties, otherwise it’s a waste of time since you cannot improve on the original.
“Best compression software” is relative, I’m afraid. Pick one from the many reviews that you can find all over the magazine sites and here on the cow and then learn how to use it. It will become the best by default. Aside from plugins or support for esoterics, the only differences between them are their interfaces and costs.
bogiesan
This is my standard sigfile so do not take it personally: “For crying out loud, read the freakin’ manual.”