What you're looking for is called a backreference (see perlre). In the pattern you'll want to use\1 (or \2 or \3...) instead of $1 (or $2 ...). On the RHS keep using $1.

while (<DATA>){
    s!</it><(.*?)><it>(.*?)</it></\1>!<$1>$2</$1></it>!g;
#                                 ^ here's the difference  
    print;
}
__DATA__
<it>a</it>+2<it>b</it><inf><it>cd</it></inf>
<it>a</it>+2<it>b</it><sup><it>cd</it></sup>
[download]

output:
<it>a</it>+2<it>b<inf>cd</inf></it>
<it>a</it>+2<it>b<sup>cd</sup></it>
[download]

Update: fixed pointer to \