If I read your code correctly, only the inner loop on $ba is sorting on values. Hash keys are not returned in a specific order, so your $foo keys may be all over the place. But your expected output really looks to be sorting on key $foo, then on $ba, so I'm not sure "sorting on values" is you are asking. If it is, I would expect the following code snippet to generate your expected output:

use strict;
use warnings;
my %hoh_test = (
    foo1 => { bar => -0.12697, baz => -0.000398154, },
    foo2 => { bar => -4.0183e-05, baz => 0, },
    foo3 => { bar => 9.966003977e-06, baz => 0.0001939, },
);
# Sort on $foo decending
foreach my $foo ( sort { $b cmp $a } keys %hoh_test ) {
    # Sort on values decending
    foreach my $ba ( 
            sort { $hoh_test{$foo}{$b} <=> $hoh_test{$foo}{$a} } 
            keys %{$hoh_test{$foo}} 
    ) {
        printf "foo: %s, ba: %s, value: %s\n", 
               $foo, 
               $ba, 
               $hoh_test{$foo}{$ba};
    }
}
[download]

The output matches your expected output:

$ perl 111142758a.pl
foo: foo3, ba: baz, value: 0.0001939
foo: foo3, ba: bar, value: 9.966003977e-06
foo: foo2, ba: baz, value: 0
foo: foo2, ba: bar, value: -4.0183e-05
foo: foo1, ba: baz, value: -0.000398154
foo: foo1, ba: bar, value: -0.12697

If instead you are sorting on $foo decending then on $ba decending, the code would instead be:

use strict;
use warnings;
my %hoh_test = (
    foo1 => { bar => -0.12697, baz => -0.000398154, },
    foo2 => { bar => -4.0183e-05, baz => 0, },
    foo3 => { bar => 9.966003977e-06, baz => 0.0001939, },
);
# Sort on $foo decending
foreach my $foo ( sort { $b cmp $a } keys %hoh_test ) {
    # Sort on $ba decending
    foreach my $ba ( sort { $b cmp $a } keys %{$hoh_test{$foo}} ) {
        printf "foo: %s, ba: %s, value: %s\n", 
               $foo, 
               $ba, 
               $hoh_test{$foo}{$ba};
    }
}
[download]

This output also matches your expected output:

$ perl 111142758b.pl
foo: foo3, ba: baz, value: 0.0001939
foo: foo3, ba: bar, value: 9.966003977e-06
foo: foo2, ba: baz, value: 0
foo: foo2, ba: bar, value: -4.0183e-05
foo: foo1, ba: baz, value: -0.000398154
foo: foo1, ba: bar, value: -0.12697

If you really want your hash output sorted by values, there may be other ways but the simplest that comes to my mind is to push the order into a temporary structure you can actually sort:

use strict;
use warnings;
use utf8;

my %hoh_test = (
    foo1 => { bar => -0.12697,        baz => -0.000398154, },
    foo2 => { bar => -4.0183e-05,     baz => 0, },
    foo3 => { bar => 9.966003977e-06, baz => 0.0001939, },
);

# Sort on values by pushing into an intermediary structure
my @ordering;
foreach my $foo ( keys %hoh_test ) {
    foreach my $ba ( keys %{ $hoh_test{$foo} } ) {
        push @ordering, { foo => $foo, ba => $ba, v => $hoh_test{$foo}
+{$ba}, };
    }
}
# Sort intermediary structure on value (v) from above.
foreach my $i ( sort { $ordering[$b]{v} <=> $ordering[$a]{v} } 0 .. $#
+ordering ) {
    printf "foo: %s, ba: %s, value: %s\n", 
            $ordering[$i]{foo}, 
            $ordering[$i]{ba}, 
            $ordering[$i]{v};
}
[download]

This also creates your expected output:

$ perl 111142758c.pl
foo: foo3, ba: baz, value: 0.0001939
foo: foo3, ba: bar, value: 9.966003977e-06
foo: foo2, ba: baz, value: 0
foo: foo2, ba: bar, value: -4.0183e-05
foo: foo1, ba: baz, value: -0.000398154
foo: foo1, ba: bar, value: -0.12697

Hope that helps.