$/ = "</address>\n";
while ( <DATA> ) {
    chomp;
    print "$_\n" for sort { $a cmp $b} split /\n/;
    print $/ if ! eof DATA;
}


__DATA__
xxx data
aaa data
<address>
<state>address1</state>
<ref refid="aff1">1</ref>
<ref refid="aff2">2</ref>
<ref refid="e2"/>
<ref refid="e4"/>
<ref refid="aff4">4</ref>
</address>
<address>
<state>address1</state>
<ref refid="aff1">1</ref>
<ref refid="aff2">2</ref>
<ref refid="e4"/>
<ref refid="aff3">3</ref>
</address>
xxx data
aaa data


##</code><code>##

xxx data
aaa data
<address>
<state>address1</state>
<ref refid="aff1">1</ref>
<ref refid="aff2">2</ref>
<ref refid="aff4">4</ref>
<ref refid="e2"/>
<ref refid="e4"/>
</address>
<address>
<state>address1</state>
<ref refid="aff1">1</ref>
<ref refid="aff2">2</ref>
<ref refid="aff3">3</ref>
<ref refid="e4"/>
</address>
xxx data
aaa data