This really seems like a job for Perl rather than a text editor's internal find/replace, especially since you're playing with parentheses; nested parens are notoriously difficult to regex properly.

The following monstrosity accounts for nested parens, and also isn't limited to the start of line; it tries to avoid messing with things that don't look like function calls. This DOESN'T work on the last example (nested function calls which need to be fixed). I'm sure there are some other quirks to Perl syntax which this doesn't catch.

use Regexp::Common qw/balanced/;

while (<DATA>) {
   chomp;

   my $bp = qr/$RE{balanced}{-parens=>'()'}{-keep}/;

   $_ =~ s{
      &?                # optional &
      (                 # capture either:
         (?<=&) \w+     #    bareword preceeded by &
      |                 # or
         \w+ (?=\s*\()  #    bareword followed by (
      )                 #
      (?: \s* (?=\())?  # optional white space, if followed by (
      (?:               # either:
         $bp            #    balanced parens
      |                 # or
                        #    nothing!
      )
   } 

   # if no second capture, supply an empty () 
   { $1 . ($2 || '()') }exg;

   print "$_\n";
}

__DATA__
&foobar
&foobar()
foobar()
&foobar("asdf")
&foobar( test(), qw(etc.))
&foobar( test(test() . test()) )
&foobar("a", 5, qw(dave jen anne matt), map({tr/[a-z]/[A-Z]/; $_;} @mi
+xedCase));
&dont_change if not &function()
&foobar ('<- white space?')
&foobar( &test_nested )
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