No. Mobipocket books are not in the same format as ereader books. Mobipocket is supposedly working on an ipod touch/iphone program so hopefully they'll have one out soon.
With ebooks, if you buy from a company they come in a DRM'd, proprietary format. Sony Reader books cannot be read by ereader or mobipocket, mobipocket books cannot be read by ereader or Sony, ereader cannot be read by mobipocket or Sony, etc.
What's confusing is that the eReader app sounds on the surface like a generic ebook reader, but it is actually a proprietary program.
I have a few mobipocket books as well, so I am hoping their program comes out soon.