G'day Joe and hapibeli,
SharpEye - http://www.visiv.co.uk/ - works very well. It's a while since I've used it so I don't remember what image formats it can read, in any case, I always used it to do the scan first so the format didn't matter. I used to save them as tif's but there were other options... Version 2 is streets ahead of version 1.

Output is in native format (.mro), MIDI, NIFF and MusicXML

They also have an SDK available for those wanting to use their technology in their own product.

--=-- My credo: If it's worth doing, it's worth overdoing - just ask my missus, she'll tell ya laugh --=--
You're only paranoid if you're wrong!