using an array is most likly faster and should require less memory for storage than a hash unless the number of gaps comprise a large part of the data. If that is the case you may wish to consider using a hash:

use warnings;
use strict;

use constant kMaxGap => 7;

my %gappyData;

/^(\d+)\s+(\d+)/ and $2 != 0 and $gappyData{$1} = $2 while <DATA>;

my $lastx;
my $lasty;

for (sort {$a <=> $b} keys %gappyData) {
    next if ! defined $lastx;
    next if ! defined $lasty;
    
    my $gap = $_ - $lastx - 1;
    
    next if $gap == 1;
    next if $gap > kMaxGap;
    next if $gappyData{$_} != $lasty;
    $gappyData{$_} = $lasty for $lastx .. $_;
} continue {
    $lastx = $_;
    $lasty = $gappyData{$_};
}

for (1 .. $lastx) {
    if (defined $gappyData{$_}) {
        print "$_, $gappyData{$_}\n";
    } else {
        print "$_, -\n";
    }
}

__DATA__
1 2
2 3
3 3
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 3
12 0
13 0
14 4
[download]

Prints:

1, 2
2, 3
3, 3
4, 3
5, 3
6, 3
7, 3
8, 3
9, 3
10, 3
11, 3
12, -
13, -
14, 4
[download]

Alternatively you can use a similar technique using missing values represented by undef in an array:

use warnings;
use strict;

use constant kMaxGap => 7;

my @gappyData;

/^(\d+)\s+(\d+)/ and $2 != 0 and $gappyData[$1] = $2 while <DATA>;

my $lastx;
my $lasty;
my $currx = 1;

for (@gappyData[1..$#gappyData]) {
    next if ! defined $lastx;
    next if ! defined $lasty;

    my $gap = $lastx - $currx - 1;
    
    next if $gap == 1;
    next if $gap > kMaxGap;
    next if ! defined $gappyData[$currx] or $gappyData[$currx] != $las
+ty;
    $_ = $lasty for @gappyData[$lastx .. $currx];
} continue {
    $lasty = $_, $lastx = $currx if defined $_;
    ++$currx;
}

$currx = 1;
for (@gappyData[1..$#gappyData]) {
    if (defined $_) {
        print "$currx, $_\n";
    } else {
        print "$currx, -\n";
    }
    ++$currx;
}
[download]

which generates the same output given the same data.