I have not used my visa card to do this or my old master card when I saw it popping up in a few places since I wasn't sure about it being able to know about transfers and such. I haven't heard anything about it, so I may just use my card in places they have when I find myself without fare on my metro card so I won't have to stop to refill it, but I do not have a iphone so that one bit I won't be able to do.
If you have let me know how it has worked out for you. The iphone app or just tapping your visa or master card in the subway or on the bus.
Lost Your MetroCard? Try Your iPhone - DNAinfo.com