For the most part, the choice of a codec is completely up to you. Every codec available has a different ratio of Quality to File size. What you intend to do with the footage will affect which one you choose. Generally, once you have added effects to your footage you will want to edit it back into your movie project in your editor. Uncompressed footage will retain the highest possible quality, but has large file sizes. The DV codecs offer a decent balance of good quality, while reducing file sizes significantly. If you are exporting for final distribution, you might want to use a codec with a higher compression ratio, like mpeg-4. If you want to retain an alpha channel when rendering, the Animation codec is the way to go.
You might also want to take a look at the Ultimate FAQ