There's an HTML validator built in to the editor and it will, by default, throw out all but the simplest HTML tags.
The Apple document, Mac OS X Server, Wiki Server Administration V 10.6 explains all the gruesome details. But here's the solution that I use:
Change to the Wiki Server's directory by using
cd /Library/Application\ Support/Apple/WikiServer
If it doesn't exist, create a file called whitelist.plist:
sudo touch whitelist.plist
The file will be owned by root and all members of the _teamserver group. The latter is required for the Wiki service to have access.
Then edit the file with any appropriate editor -- I like vi:
sudo vi whitelist.plist
The file needs to have very specific formatting. This one should get your YouTube embedded HTML working:
protocols
scp
styles
font-size
tags
object
width
height
param
name
value
embed
src
type
width
height
script
hr
After making changes or additions, save and close the whitelist.plist file then restart the Web service using the Server Admin application.
If you aren't at all familiar with vi, then you may want to instead create a text file on your desktop, put the content into it, then move it to the right location and change its ownership and permissions.
Hope this helps.