I'm thinking of things like $VERSION and @ISA.

These kind of things are fine, you are only declaring them with our for your own convenience within your module - when they are accessed by perl itself or by another module (in the case of $VERSION and ExtUtils::MakeMaker for instance,) they are accessed as if they were fully qualified. Infact h2xs does declare them as our by default :

our @ISA = qw(Exporter);

#  .. removed the comments

our %EXPORT_TAGS = ( 'all' => [ qw(

) ] );

our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );

our @EXPORT = qw(

);
our $VERSION = '0.01';
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/J\