I've recently been creating a lot of zip files. Now, for this purpose the output has to be a regular zip file - readable by all the zip tools out there, including older versions and the jar utility. Change format and you can get better compression, for sure, but you're not compatible with all the existing tools. That rules out the bzip2 support in newer versions of zip and unzip, as well.
To create a zipfile with the zip command is basically:
zip -9 -q -r output.zip input_files ...
Now, p7zip can also create zip files (and others) that are absolutely compatible.
7za a -tzip -mx=9 -mfb=256 output.zip input_files ...
On my test data, this gives an additional 4% over the best that zip can do. Might not sound much, but on a CD-sized iso image that's an additional 30M of data you can squeeze in.
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