I use Navigon for iPhone. It has a setting under Route Profile that allows you to select Car, Motorcycle, Bicycle, or Pedestrian.

I use an Evotek 4lock mounting system to securely mount the phone to the bike.

I'm not sure why you would want to map your own route and load it on the phone since Navigon will map out bike-specific turn-by-turn directions for you but there is an article out there on google that describes back-loading a custom route into Navigon on a jail-broken iPhone. Personally, I don't see the need as the app already does it for you.

That being said, I rarely use turn-by-turn; rather, my day-to-day app is Cyclemeter.