Gentle forestcreature: I strongly endorse the wise advice of others to use a proper HTML parser, but here's another (very) naive regex approach using the Special Backtracking Control Verbs of 5.10+ (see perlre):

>perl -wMstrict -le
"my $s =
   qq{foo\nbar\t<pRe> no\nnot\tnever </PrE> x\ty\nz };
 ;;
 my %replace = (
   qq{\n} => '<br/>',
   qq{\t} => '&nbsp; &nbsp; &nbsp;',
   );
 ;;
 my $pre = qr{ (?i) <pre> [^<]* </pre> }xms;
 ;;
 print qq{[[$s]]};
 $s =~ s{ $pre (*SKIP) (*FAIL) | ([\n\t]) }{$replace{$1}}xmsg;
 print qq{[[$s]]};
"
[[foo
bar     <pRe> no
not     never </PrE> x  y
z ]]
[[foo<br/>bar&nbsp; &nbsp; &nbsp;<pRe> no
not     never </PrE> x&nbsp; &nbsp; &nbsp;y<br/>z ]]
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