Have a look at
RawRead,
DevBlocks and Transdisk for simple CLI-driven tools to read/write Amiga disks to/from real floppies and ADF images.
Note: any tools involving writing of Amiga disks will have to be run on a real Amiga (for obvious reasons regarding PC disk controllers).
Or, if you're serious about Amiga/PC disk transfer, you can buy a Catweasel - a PCI-based disk controller card that'll let you use a standard PC 1.44Mb drive to read/write Amiga disks.
Finally, has anyone tried getting AmiKit to run on real hardware? I'd be interested in the results...
- Ali