I don't how well this will wrap but, here's an expansion, with odd quoting constructs removed and regexes expanded. Over all, I'd say this was a bit too easy to unravel, you haven't really abused any features

$_='&u&J&t&s';
@_=split(/\&/);        # @_ = qw(\nu J t s);
$_=join('',@_);        # $_ = '\nuJts';
s/                     # regular expression on $_
  \s*                  # 0 or more whitespace, matches \n
  (.)                  # character, into $1
  (.)                  # character, into $2
/
  $2$1                 # switch the characters
/gx;                   # $_ = 'Just'
$_.=' %a%n%o%t%h%e%r'; # $_ = 'Just %a%n%o%t%h%e%r'
s/\%//gx;              # get rid of those %, $_ = 'Just another';
$_.='|e|P| | |l|r';    # $_ = 'Just another|e|P| | |l|r'
s/                     # regex on $_
  \|(.)                # | then char => $1
  \|(.)                # | then char => $2
  \|(.)                # | then char => $3
/
  $3$2$1               # put the three chars back, in reverse
/gx;                   # $_ = 'Just another Perl '
$_.='CHARKE.', "\n";         # $_ = 'Just another Perl CHARKE.\n'
s/
  ([A-Z])([A-Z])([A-Z])# Three capital letters in a row, into $1,$2,$3
/                      # replaced with
  \L$2$3$1\E           # their lower case equivilients,
                       # in a different order
/gx;
s/\n//g;               # remove any \n
$_.=$/;                # add a newline to $_
print;                 # print "Just another Perl hacker.\n"
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