When you say "save" do you mean render?
If so, read through this. The rest of the section wouldn't hurt.
Although I would also like to say that AE's not the best program for producing compressed files. A lot of codecs can take advantage of multi-pass compression which results in higher quality video in smaller file sizes, but After Effects doesn't do multi-pass.
My friend Dave LaRonde from CreativeCOW.net explains it in a little more detail:
Dave's Stock Answer #3
Don't use AE to compress files for final delivery. The various compressors are there only to make quick 'n dirty files showing a project's progress to producers, clients, the kids, etc. AE is incapable of doing multipass encoding, a crucial feature that greatly improves the image quality of H.264 and MPEG-type files in particular.
Render a high-quality file from AE, and use a different application to do the compression. Popular ones are Adobe Media Encoder, Sorenson Squeeze and Apple's Compressor, which comes bundled with Final Cut Suite. Even compressing in Quicktime Pro is better than compressing in AE.
Making good-looking compressed files is almost as much an art as it is a science. It is NOT straightforward at all.