Valid Through The Ages

Revised answer for "better" scoring system

C89 / C99, Score: 0

My program is 52 characters long and uses the same mechanism as in my original answer to achieve the different output. This works because C89 doesnt treat // as a comment:

i=32;main(){putchar(i+++0//**/
+52)&&i<84&&main();}

The results:

$ ./diff2c89
 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRS
$ ./diff2c99
TUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~⌂Çüéâäàåç
$ ./diff2c99 | wc
      0       1      52
$ ./diff2c89 | wc
      0       1      52
$ wc diff2.c
      1       2      52 diff2.c

Old answer:

C89 / C99, Score: -Infinity?

I'm not entirely sure if this program doesn't break the rules, but never mind. This program exploits the fact that in C89 // is not a valid comment but /* ... */ is.

Using the comment trick an other function is executed. In C89 the function just prints "trolololol..." until the stack overflows (so it might finish within 2 seconds).

f1(){printf("ol");f1();}
f2(){printf("oll");}
main(){
    printf("tr");
    void (*f[])() = {f1,f2};
    f[0 //* trollololol */
      +1]();
}

C99

$ ./diffc99
troll

C89

$ ./diffc89
trolololololololololololololololololololololololololololololololololololololololololo
lolololololololololololololololololololololololololololololololololololololololololol
ololololololololololololololololololololololololol ....

Python - 10 points less than the next best answer

print(range(100))

In Python 2, this will print the entire list of integers from 0 to 99.

In Python 3, range is a generator and so it will print only "range(0,100)".

Seeing as I've never run into a size limit on numbers in Python, I can replace that 100 with a much bigger number (2**1000, for example) and end up with a virtually infinite difference in the output.

Edited to reflect the fact that, while I can get a score that is infinitely low for any practical purpose, I cannot reach actual infinity with a program that terminates under 2 seconds

For the updated tie-breaker scoring system, I'd submit:

print(range(4))

Output:

Python 2: [0, 1, 2, 3]

Python 3: range(0, 4)

The first print has 5 unique characters ([123]), the second print has 8 unique characters (range(4)), the difference in length of output is 1, the code has 15 characters, the shortest output is 11 characters... these rules are pretty confusing but I think this brings me to a final score of 15+1-min(11,5+8) = 5.

Python - 0 points

No idea how this one works :P Just stumbled upon it while trying out random code.

int

On Python 3, it's <class 'int'> and on Python 2, it's <type 'int'> (using interative console)
"Better" Score: 3 (length) + 1 (char diff.) - 4 (unique chars)

Older Python 1 - 7 points

print()

Big thanks to @grc for this version and helping me subtract four points !

In Python 2, this statement is interpreted as print () which prints the empty tuple ().
In Python 3, the print is a function and results in nothing being printed.
"Better" Score: 7 (length) + 2 (char diff.) - 2 (unique chars)

Older Python 2 - 13 points:

print(1,2)

"Better" Score: 12 (length) + 2 (char diff. o/p) - 1 (unique chars o/p)

I know this isn't going to win but still gave an answer, as this is my first Python try :)