Just off the top of my head and having no idea how to get the windowdomain out of the output of nbtstat, what about:

use strict;

open IP,"<IP.txt" or die "Couldn't open IP.txt, $!";
while(<IP>)
{
  chomp; # does the while form of <> autochomp? I don't remember =[
  my $out = `nbtstat -A $_`;
  if($out=~/WORKGROUP\s+<(\d+)>/)
  {
    my $domain = $1;
    #do something
  }
}
[download]

My version of nbtstat, when run on myself, gave me this output:

C:\LiteStep>nbtstat -A 192.168.1.2

Local Area Connection:
Node IpAddress: [192.168.1.2] Scope Id: []

           NetBIOS Remote Machine Name Table

       Name               Type         Status
    ---------------------------------------------
    H4X0R-B0X      <00>  UNIQUE      Registered
    WORKGROUP      <00>  GROUP       Registered
    H4X0R-B0X      <20>  UNIQUE      Registered

    MAC Address = 00-02-E3-14-A4-C5
[download]

I have no real idea what those numbers in the pointy brackets are, but I decided to capture them in my regex anyways. My version above just searches through the entire output for anything that matches the regex /WORKGROUP\s+<(\d+)>/ and then sets the $domain variable. However you could also easily do something like for(split/\n/,$out){ #operate on each line }.