I see what you are trying to do here. The while ( <DATA> ) loop iterates through lines of the data file, and then you are creating more lines inside the loop that you want to iterate through them as if they were additional lines in the data file. Unfortunately, you would have to add them to the actual data file for that effect. To do what you want, you can add another loop to iterate through the new lines you've added:

!/usr/bin/perl

use strict;
use warnings;

my $title;
while ( <DATA> )
{ 
  chomp;

  if ( /\(\w+\-\d+\)$/ )
    { $title = $_; }
  else
  { 
    s/(?:^|\s)(\d\-\d\w{2}(?:\.\w+)?|[A-Z]\d{2}(?:\.\d+)?)/\n$1/g;
    foreach my $line ( split ( "\n" ) )
    { 
      next if $line !~ /^(\d\-\d\w{2}(?:\.\w+)?|[A-Z]\d{2}(?:\.\d+)?)/
+;
      print "$title;$line\n";
    }
  }
}

__DATA__
Titel Text (A12-3)
3-123.7 Just another text 3-123.8 Some more text
A12.34 Another item B56.78 Yet another item
Another Titel Text (B23-9)
1-22a.b Just another text
2-3cd.e Some more text
W12.34 Another item
Z56.78 Yet another item
Some trash
Some trash
[download]

Output:

Titel Text (A12-3);3-123.7 Just another text
Titel Text (A12-3);3-123.8 Some more text
Titel Text (A12-3);A12.34 Another item
Titel Text (A12-3);B56.78 Yet another item
Another Titel Text (B23-9);1-22a.b Just another text
Another Titel Text (B23-9);2-3cd.e Some more text
Another Titel Text (B23-9);W12.34 Another item
Another Titel Text (B23-9);Z56.78 Yet another item
[download]