Python (56)

f=lambda n,k:k<1and 1or f(n-1,k-1)*n/k;print f(*input())

Python (56)

f=lambda n,k:k<1and 1or f(n-1,k-1)*n/k;print f(*input())

Ungolfed code and some explanation of a shortcut for calculating the binomial coefficient. (Note: There is some insight that I just haven't figured out in order to get down to the 39 char version; I don't think this approach will get you there.)

# Since choose(n,k) =
#
#     n!/((n-k)!k!)
#
#          [n(n-1)...(n-k+1)][(n-k)...(1)]
#        = -------------------------------
#            [(n-k)...(1)][k(k-1)...(1)]
#
# We can cancel the terms:
#
#     [(n-k)...(1)]
#
# as they appear both on top and bottom, leaving:
#
#    n (n-1)     (n-k+1)
#    - ----- ... -------
#    k (k-1)       (1)
#
# which we might write as:
#
#      choose(n,k) = 1,                      if k = 0
#                  = (n/k)*choose(n-1, k-1), otherwise
#
def choose(n,k):
    if k < 1:
        return 1
    else:
        return choose(n-1, k-1) * n/k

# input() evaluates the string it reads from stdin, so "5,2" becomes
# (5,2) with no further action required on our part.
#
# In the golfed version, we make use of the `*` unpacking operator, 
# to unpack the tuple returned by input() directly into the arguments
# of f(), without the need for intermediate variables n, k at all.
#
n, k = input()

# This line is left as an exercise to the reader.
print choose(n, k)