When getting my injector pump reset on my 300TDi a year or so back I asked the service guys about running biodiesel. They were pretty negative and showed me service notice from Bosche stating that they would not warantee pumps that had been running biodiesel.
I think much of the concern was the back-yard productions that were turning out inconsistent quality fuels. I've swapped emails with a guy in WA who has been running his 300TDi defender for 5 or so years and swares by it.
wrt the "cleaning of the pipes" - I've heard biodiesel described as a very low strength paint-stripper - softenes and clears out a lot of stuff aparently.
Cheers,
