This seems to be exposing some weird edge cases in perl. I added some extra alias/reference tests like these:

sub by_alias { $_[0]  =~ s/\s+//; }
sub by_alias2 { for ($_[0]) { s/\s+//; } }
sub by_alias3 { ${\$_[0]} =~ s/\s+//; }
sub by_ref { ${ $_[0] } =~ s/\s+//; }
sub by_ref2 { for (${ $_[0] }) { s/\s+//; } }
[download]

I then bumped up the string size so it went in 10k increments rather than 1k, and reduced the loop count. There's a weird effect occuring when the string size switches between 130k -> 140k.

Length of string: 130000
          Rate  alias   ref2 alias2    ref alias3
alias  17544/s     --   -67%   -67%   -68%   -68%
ref2   52632/s   200%     --    -0%    -5%    -5%
alias2 52632/s   200%     0%     --    -5%    -5%
ref    55556/s   217%     6%     6%     --     0%
alias3 55556/s   217%     6%     6%     0%     --

Length of string: 140000
          Rate alias3 alias2   ref2    ref  alias
alias3  1376/s     --    -0%    -0%    -0%   -92%
alias2  1377/s     0%     --    -0%    -0%   -92%
ref2    1379/s     0%     0%     --    -0%   -92%
ref     1381/s     0%     0%     0%     --   -92%
alias  16393/s  1092%  1090%  1089%  1087%     --
[download]

That's just bizarre. It seems for strings < 130k, something strange is occuring with @_ aliasing, and for strings > 130k, for () aliasing and references are going haywire. Very odd indeed. This is debian perl, v5.8.8 built for i486-linux-gnu-thread-multi