Co-Founder of Embark here (letsembark.com). We have apps for 12 systems, mostly in the US (BART, Caltrain, NYC, LIRR, MNR, NJT, DC Metro, Philly, CTA, Metra, Boston & London Tube). We also integrate with iOS 6 maps, so our apps should show up for you if they're relevant. In my subjective opinion, it's a way better experience than a google maps web view. EDIT: Looks like my co-founder David beat me to the punch
I love Google Transit directions. Can you give some examples of where Embark beats out Google Transit (screenshots if possible)? Also do you have real-time updates on arrival times with SF Muni? Google Transit does not.
Currently we don't have an app for muni, though it's something we're working towards. There are some nice apps for Muni that have real-time arrivals but lack routing. Transporter & Routsey are probably the two best.