Theres no hard and fast rules for me, generally IMO lexicals should be declared at the begining of the closest scope to where they are used. And unless a variable is deliberately intended to be a static for a closure then all sub declaration should precede any lexical declarations at the file scope, and the latter (lexicals at file scope) should be avoided outside of snippets. So for instance your code in version two would get wrapped in a subroutine almost instantly.

But the reason these are general is that I think there are two issues in chosing this placement, what the variable is used for and transfering the authors intentions. If I see:

my $sum=0;
while (<>) {
  ...
  if ($blah) {
    my $foo=somefunc;
    something($foo);
  }
}
[download]

Then I know $foo is a throwaway, and $sum is a "working" var of some sort (poor thing should get off the streets :-). Other arangements are to declare a set of vars in such a way its clear that they are fields in a record or the like. All in all, whatever is readable and self documenting is good in my book.