It's wrong to use \1 in the substitution expression. You need to use $1.

Your code doesn't even compile. / in </TAG> needs to be escaped.

Once I fix those, it works for me.

use strict;
use warnings;

my $text; { local $/; $text = <DATA>; }
$text =~ s/\#\#\#\n\[b\](.+)\[\/b\]/<TAG>$1<\/TAG>/g;
print $text;

__DATA__
###
[b]word[/b]
text
###
[download]

<TAG>word</TAG>
text
###
[download]

i guess that's because windows uses the combination "end of line+cr"

No. When reading a file, CRLF will be converted to LF automatically on read unless you tell it otherwise.