my @highlights = (
    'foo',
    'bar',
    'baz',
    '\w*a\W+my\w*',   # the ...a my... phrase example
);
my $re = join '|', @highlights;
$re = qr/\b($re)\b/i;

local $/ = "\n\n";   # read in a para at a time
while(<DATA>){
    s/$re/uc $1/ge;
    print;
}

__DATA__
Hello Foo,

This is your friend Baz wondering
if you would like to go to the bar
to talk server foo. Barclays is a 
foobar bank BTW.

So a Perlmonk and a Panda walk into a bar.
Know I know you think this is going
to be a joke but I saw the panda 
myself!