From what I've gleaned off the show because I have watched a few episodes when I was bored or had them on in the background while I was waiting for Venture Brothers to come on back in the day, I think the big joke about Stewie is that he's obviously gay and so he crossdresses and acts feminine and let's very gay things about himself slip.
Because nothing's funnier than a toddler who wants to have somebody sodomize him! Wokka wokka!