Rotate Cartesian coordinates.

Perl, 112 80 78

s/\S*//;$c=cos$&;$s=sin$&;s/([^ ,]*),(\S*)/($1*$c-$2*$s).",".($1*$s+$2*$c)/ge

Run on command-line as perl -pe 'code here', p option counted in code size.

For reference, here's my previous approach. But regexes are too damn powerful.

split/[ ,]/,<>;$_='A;Y,print$x*cos($a)-$y*sin$a,",",$x*sin($a)+$y*cos$a,$"whileX';s/[AXY]/\$\l$&=shift\@_/g;eval

Python (157)

from math import*;f=float
i=raw_input().split();a=f(i[0])
c=cos(a);s=sin(a)
def p((x,y)):print"%f,%f"%(c*x-s*y,s*x+c*y),
for l in i[1:]:p(map(f,l.split(',')))

C (124 Characters)

main(){double t,x,y,c,s;scanf("%lf",&t);c=cos(t);s=sin(t);while(~scanf("%lf,%lf",&x,&y))printf("%lf,%lf ",c*x-s*y,s*x+c*y);}