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You'll want to export your video either for further processing in other applications (e.g., Photoshop CS4 Extended, or later version of same) or for presenting to an audience. Which output codec to use depends on your target device or application. For further processing you need to use the highest quality codec possible (e.g., Apple ProRes HQ).
If you want to present your movie to an audience, there are at least two options. You can produce the final compressed version (e.g., for the Internet), or prepare a version for Blu-Ray or DVD production. For Blu-Ray, you should use a high quality codec; otherwise you may end up compressing twice because the Blu-Ray rendering process is compressing again.