I have to agree with Greg on this one, Routsey 2.o for the iPhone is a brilliant application. It melds together real time BART information with Muni making it really easy to get around the city. The best thing in my mind is the ability to bookmark stops you visit often. That is worth the $2.99 right there.
One of the things that we found out BART does better than anyone else is releasing thier real time data into space. Anyone can have access to it which is rare for transit agencies to be that transparent. Kudos to the team there for such excellent foresight that other agencies don't even want to even think about.