I am still thinking about how to deal with the collection that I have in Aperture.
And before you respond with "just keep the files" or "export the files and import into Lightroom", it's no longer 1999 and it's not just about the files. There is metadata, tags, collections, stacks, and other kinds of organizational structure that are not easily reflected in a directory hierarchy.
I've been bitten once, I won't be fooled again — this time I intend to develop my own solution for keeping this data in the long term.