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    <p>I don't see how encoding an arbitrary set of bits differ from compressing/encoding any other form of data. Note that you only impose a loose restriction on the bits you're encoding: namely, they are lists of lists of bits. With this small restriction, this list of bits becomes just data, arbitrary data, and that's what "normal" compression algorithms compress.</p> <p>Of course, most compression algorithms work on the assumption that the input is repeated in some way in the future (or in the past), as in the LZxx family of compressor, or have a given frequency distribution for symbols.</p> <p>Given your prerequisites and how compression algorithms work, I would advice doing the following:</p> <ol> <li>Pack the bits of each list using the less possible number of bytes, using bytes as bitfields, encoding the length, etc.</li> <li>Try huffman, arithmetic, LZxx, etc on the resulting stream of bytes.</li> </ol> <p>One can argue that this is the pretty obvious and easiest way of doing this, and that this won't work as your sequence of bits have no known pattern. But the fact is that this is the best you can do in any scenario.</p> <p>UNLESS, you know <em>something</em> from your data, or some transformation on those lists that make them raise a pattern of some kind. Take for example the coding of the DCT coefficients in JPEG encoding. The way of listing those coefficients (diagonal and in zig-zag) is made to favor a pattern in the output of the different coefficients for the transformation. This way, traditional compressions can be applied to the resulting data. If you know something of those lists of bits that allow you to re-arrange them in a more-compressible way (a way that shows some more structure), then you'll get compression.</p>
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