OK, I have done some web searching, in one of the chat groups, some one looked up the Technical Manual for the Enterprise and there is only 1 bathroom in the entire ship. I can not imagine the queues for that bathroom.
Also some one else posted the following
"I remember a startrek special along time ago(hosted by jonathan frakes) and he answered that question saying there was a bathroom and he pointed somewhere but cant remember the location."

Here is the thread
http://www.gamedev.net/community/forums/topic.asp?topic_id=201035&whichpage=2

This leads me to one conclusion, they must transport it directly from the crews body (must be using those Transporter Bio Filters), but still leaves the other question open, transport to where. (OK - "Beam them out Scotty").

Interesting
Wayne