Transposed, primes, oh my!

C, 2*70 2*60

Prints y for primes, nothing otherwise.
EDIT: Changed code to save 10 chars. Must be run without paramters (so m=1).

main(m,n){for(scanf("%d",&n);n%++m&&n>1;);n-m||puts("y");}/*
\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\*/ 

The method for handling the transposition is quite generic, and can be applied to any program.
It's based on converting this:

abcd/*
\\\\*/

To this:

a\
b\
c\
d\
/*
*/

And both mean simply abcd.

C - 13x13

Reads the input from stdin and prints a 1 for prime and a 0 for not prime.

////m(i;(a=)<
////aans")a;2
//:Di)tc%;;p)
//O n{ adfau+
main//bn"o%t4
(a){///f,r-c8
int b///&(-h)
;scanf///bba;
("%d",&///;r}
a);for(b///( 
=a;a%--b;//( 
);putchar((b 
<2)+48);}    

edit: compiles with gcc and clang now, other compilers weren't tested

C, 12x12 chars

A two-dimensional solution, unlike my other answer, based on the same code (and like it, prints y for prime, nothing for composite).
The structure is similar to Quasimodo's answer, but my code is shorter, and I think my usage of comemnts is a bit more efficient, so I can fit 12x12.

////m()s";np
////am{c%n>u
////i,fad%1t
////nnon"+;s
main//rf,+)(
(m,n//((&m;"
){for(//n&ny
scanf(//)&-"
"%d",&n)//m)
;n%++m&&//|;
n>1;);n-m|| 
puts("y"); }