If I Had Intelligently Designed Man...

VoidEater

...I'd leave out stuff that serves no purpose - like the appendix and coccyx.
...I'd make the testicles internal so all those baseballs in the groin didn't hurt so much.
...I'd add a third hand and eyes in the back of the head.
cofty

I would not wrap the prostate around the urethra - 47 so far so good
VoidEater

^ Ha! I forgot that one! Me - not so lucky/fortunate/blessed...!
keyser soze

I'd make every penis the same size, so there'd be no envy.
cofty

Maybe a bit less proximity between the wind pipe and the food pipe - Cofty; still traumatised from almost chocking to death as a child (for you Brits it was a Pan Drop)
leavingwt

I would design the airway in a manner in which food could not enter into it, resulting in death by choking.
pixiesticks

This! :P