as you ask for the "best way" and already mention "versioned" i assume that you have some version control (as opposed to eclipses "local history" involved. basically, it's "best practice" to have version control, even when working alone. use this and you're done.
this enables you not only to migrate to a new machine (as you mentioned in a comment to matt b's question) but to operate on both - the old and new machine - simultaneously should you discover that you rely on some external component only available in the old environment. this will also help you to get your workspace&repository clean of hardcoded library paths and rather rely on logical library names.
maybe i'm missing something, but wouldn't you just start eclipse, and either select the new workspace to use or select
switch workspace from the
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