With arrays for ordering instead of IxHashes:

#!/usr/bin/perl
use warnings;
use strict;

my %hash;
my @projects;
my %vitems;

while (my $buf = <DATA>) {
   chomp($buf);
   my ($vitem, $project_info) = split(/,/, $buf);
   my ($project_name, $segment_info) = split(/\|/, $project_info);
   my (@segments) = split(/;/, $segment_info);
   push @projects, $project_name unless exists $hash{$project_name};
   push @{$vitems{$project_name}}, $vitem;

   push(@{$hash{$project_name}{$vitem}}, @segments);
}

for my $proj (@projects) {
    print "Project: $proj\n";
    for my $vi (@{$vitems{$proj}}) {
        print "  VItem: $vi\n";
        for my $seg (@{$hash{$proj}{$vi}}) {
            print "    Segment: $seg\n";
        }
    }
}

exit(0);

# -----------

__DATA__
J_071117,BM:3|12.0-25.2;32.9-88.0
J_070424,BM:3|625-920;1017.905-1178
J_021212,BB:1|123-166;409-455
070526,SWT:1|53.160-59.320;77.720-86.120;370.800-416.800
070609,SWT:1|713.760-1159.200
070616a,SWT:1|0.0-652.0
070616b,SWT:1|401.40-461.800;483.160-490.640;503.400-595.200;602.440-6
+95.400;699.200-882.400
J_071019a,SWT:1|372.925-910.385;927.620-1038.830
J_071019b,SWT:1|268.15-808.330
J_071025,SWT:1|936.215-1659.635
071123_F,SWT:1|45.4550-81.665
[download]