I've used Devel::SmallProf and Apache::SmallProf (mod_perl profiler) with good success. These profilers will tell how much time was spent on each line executed, as opposed to Devel::DProf, which I understand outputs time spent on each subroutine.

BTW, I used Apache::SmallProf to profile a very large mod_perl application and it was giving me a segmentation fault when logging subroutine calls. I had to "fix" this by commenting out the "sub sub" method in the profiler source code, so it no longer logged subroutine calls. I only saw this problem when profiling the large application. I couldn't spend time on finiding what was it that made it crash. If someone knows about this problem I'd be glad to learn from him/her.