Why not use a hash? 
#!/usr/bin/perl -w

use strict;

my $html = <<END_OF_HTML;
Hello! oX
World!

<;<;<;<;

Hi!
Samn! (~)
END_OF_HTML

my %emotes = map {split /#####|\n/} <DATA>;

for my $entry(keys %emotes) {
        $html =~ s!\Q$entry\E!<img src="$emotes{$entry}.gif">!g;
}

print $html;

__DATA__
oX#####skullandbones
<;#####pie
(o)#####goatse
(~)#####ninja

[download]
Note that im removing the trailing newline in the split operation, which is -ew- ugly.

In reply to Re: Search and replace with special characters by io
in thread [untitled node, ID 202198] by Samn

Title:
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