I tend towards the second and third options. Each file has its own version number which gets bumped, e.g., from 1.0.0 to 1.0.1 each time it's modified. Once I'm ready to issue the next release, I sync all version numbers to 1.1.0 and go from there for further changes.

Aside from this generally making sense to me, it makes it easy when a client reports a problem that I thought I fixed last week - "What version of Foo::Bar.pm are you using?" "1.0.1" "Still? I sent you 1.0.4 last night... Here's a fresh copy of it." - without having to start diffing his version of the code against mine or hoping I notice that it's a stale version before spending too much time trying to isolate the "new" bug.