I'll play my part here and toss out some ideas we could use this for.
I'm not really advocating it, yet, but I'll say I am

We could break up the code into multiple sections and allow alternatives
for sections with different versions. Different versions could be used
for a few different things, including different optimization levels,
supporting multiple bytecode versions, or storing both pre and post AST
transformations of the code.

Meta-ish data like docstrings could be pulled out of the code objects
and injected in non-optimized modes. This might also include original
source for code, which could be helpful when you change the source and
still-running code tracebacks and gives you invalid lines.

Bookkeeping data could sit in some sections, detailing things like call
stats (average call time, frequency, etc) and other information that
could be useful for optimizers and JIT compilers like psyco.