I imagine there's a more efficient way to do this with backwards or forwards looking, but I'm not that good at regex. The following works, even if it does more substitutions than are necessary:

$_ = join '', <DATA>;

# Add & to front of function calls without.
s/&?(\w+\(.*?\))/&$1/g;

# Add () to end of function calls without.
s/(&\w+)(?:\((.*?)\))?/$1($2)/g;

print;

__DATA__
&somesub('args');
somesub('args');
&somesub;
[download]

This way of doing things may have problems, however. You will end up not only replacing sub calls, but built-in function calls as well. You need to add a sub to check function names against a Perl function list, and add that to the regex with an e flag.