If you have seen this error "Service 'MsExchangeTransport' failed to reach status 'Running' on this server" during exchange installation setup on Win 2008 check to see if you have done the following.
Check both of these:
Well if you have either situation then this is the likely cause of your problem.
Doing this from the command prompt may be easier
Trying to kill the service and do anything manually to it doesnt make a difference..
Reboot the machine and reinitiate the setup
Fingers crossed and this does the trick - hopefully it helps ;-)
If not there is a transport forum available from Microsoft at http://forums.microsoft.com/TechNet/ShowForum.aspx?ForumID=844&SiteID=17
update 19/01/09 if this fails ref my blog item. this will work
Exchange 07: Topology discovery failed, error 0x80040a02 (DSC_E_NO_SUITABLE_CDC)